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Optogenetic tools for inducing organelle membrane rupture

Editorial note: Randomized controlled trial of early, small-volume formula supplementation among newborns: a study protocol

Theoretical analysis of low power optogenetic control of synaptic plasticity with subcellular expression of CapChR2 at postsynaptic spine

Study on air-pipe cooling effect and cooling strategy of mass reinforced concrete wall

Coherence analysis of local randomness and nonlocal correlation through polarization-basis projections of entangled photon pairs

New insights into the cultivability of human milk bacteria from ingestion to digestion and implications for their Immunomodulatory properties

Abstract Human milk (HM) microbiota is increasingly studied for its potential health benefits. However, the physiological state of HM bacteria and consequently their effects on gut homeostasis remain a question. This study investigated the physiological state of the HM microbiota by characterizing its cultivable fraction as it might be at the point of ingestion and assessing the effects of digestion, in the specific context of the immature infant digestive tract, on the cultivability and immunomodulatory properties of six HM strains representative of prevalent genera in HM. Twenty-eight HM samples were analysed by 16 S metabarcoding either directly on raw milk (raw milk microbiota, RM) or on the complete cultivable fraction obtained from seven non-selective media (cultivable milk microbiota, CM). This approach enabled a more in-depth investigation of CM than conventional methods based on the individual sequencing of a subset of isolates and resulted in a moderate gain in diversity within each HM sample. It confirmed that diversity was lower in CM than in RM, with ~ 7 versus 69 genera per sample in CM and RM respectively, and an under-representation of strictly anaerobic genera in CM. In vitro infant gastrointestinal digestion resulted in overall good survival of the 6 HM strains but partial or complete loss of their immunomodulatory properties on the monocyte THP1 cell line, except for a Staphylococcus epidermidis strain that gained immunomodulatory potential. These results highlight the potential of HM bacteria to survive during the infant gastrointestinal digestion and interact with the intestinal epithelium and immune system, as well as the importance of considering the digestion process when evaluating host-bacteria interactions.

How scale affects N2O emissions in heterogeneous fields of a diversified agricultural landscape

Abstract Nitrous oxide (N2O) emissions from agricultural soils vary due to factors such as soil organic matter, soil moisture, and crop type, leading to short-term variations and concentrated zones of high emissions, known as “hot moments” and “hotspots.” These peaks, occurring at various scales, contribute significantly to total N2O emissions. This is particularly relevant for sandy soils, where high porosity and low water-holding capacity promote gas diffusion and create moisture variability, leading to highly heterogeneous N2O emissions. We investigated N2O fluxes along a transect in six agriculturally used patches (0.52 ha) with varying texture, yield potential and crop rotation. We measured N2O fluxes bi-weekly over 2 years, using a non-flow-through non-steady-state (NFT-NSS) manual closed chamber system, covering different crops and weather conditions. Hot moments accounted for 6–71% of total crop N2O emissions and were mostly driven by soil physical properties. On a small scale, soil texture and environment determined spatial heterogeneity of N2O emissions being more pronounced for sandier soils. On patch level, N2O emissions differed more strongly than on microplot level and were mainly driven by crop-type and management. Our findings highlight the importance of accounting for intrinsic variability in soil texture, topography, and microclimate within patches. Additionally, broader differences across management-influenced patches must be considered to better understand the drivers of N2O emissions. This dual-scale approach emphasizes the need for high-resolution soil monitoring for mitigation strategies and to refine models. At the same time, it guides farmers toward soil-specific fertilization to reduce emissions and maintain yields in diverse agricultural landscapes.

Monocular depth estimation via a detail semantic collaborative network for indoor scenes

Association between subretinal fluid duration in central serous chorioretinopathy and chorioretinal structure in unaffected fellow eyes

Computational discovery of natural inhibitors targeting enterovirus D68 3C protease using molecular docking pharmacokinetics and dynamics simulations

Abstract Enterovirus D68 (EV-D68) is a significant global health threat, responsible for severe respiratory and neurological complications, with no FDA-approved antiviral treatments currently available. The 3C protease of EV-D68, an essential enzyme involved in viral replication, represents a key target for therapeutic development. In this study, we employed a comprehensive computational approach, including molecular docking, pharmacokinetic predictions, and molecular dynamics simulations, to identify potential natural inhibitors of the EV-D68 3C protease. Screening a library of natural compounds, Withaferin-A (CID: 265,237) and Baicalin (CID: 64,982) emerged as top candidates due to their favorable pharmacokinetic profiles, high binding affinities (-10.7 kcal/mol for Withaferin-A and -9.5 kcal/mol for Baicalin), and interactions with key residues in the protease’s active site. The molecular dynamics simulations demonstrated the stability of the protein–ligand complexes, with low root mean square deviation (RMSD) and fluctuation (RMSF) values over a 100-ns trajectory. Free energy calculations further supported the superior binding efficiency of Withaferin-A. These findings suggest that Withaferin-A and Baicalin have significant potential as natural inhibitors of EV-D68 3C protease, offering a promising foundation for future experimental validation and the development of targeted antiviral therapies against EV-D68.

Carboxylic acids dendrimer functionalized magnetic nanoparticles for carbohydrates conversion to 5-hydroxymethylfurfural

Computational network biology analysis revealed COVID-19 severity markers: Molecular interplay between HLA-II with CIITA

COVID-19, severe acute respiratory syndrome coronavirus 2, rapidly spread worldwide. Severe and critical patients are expected to rapidly deteriorate. Although several studies have attempted to uncover the mechanisms underlying COVID-19 severity, most have focused on the perturbations of single genes. However, the complex mechanism of COVID-19 involves numerous perturbed genes in a molecular network rather than a single abnormal gene. Thus, we aimed to identify COVID-19 severity-specific markers in the Japanese population using gene network analysis. In order to reveal the severity-specific molecular interplays, we developed a novel computational network biology strategy that measures dissimilarity between networks based on the comprehensive information of gene network (i.e., expression levels of genes and network structure) by using Kullback–Leibler divergence. Monte Carlo simulations demonstrated the effectiveness of our strategy for differential gene network analysis. We applied this method to publicly available whole blood RNA-seq data from the Japan coronavirus disease 2019 Task Force and identified differentially regulated molecular interplays between 368 severe and 105 non-severe samples. Our analysis suggests the gene network between HLA class II, CIITA, and CD74 as a COVID-19 severity specific molecular marker. Although the association between HLA class II and COVID-19 has been demonstrated, our data analysis revealed that the molecular interplay of HLA class II with its target and/or regulator is a crucial marker for COVID-19 severity. Our findings from computational network biology analysis suggest that suppression and activation of the molecular interplay between HLA class II, CIITA, and CD74 provide crucial clues to uncover the mechanisms of COVID-19 severity.

Shear behavior of prefabricated steel–concrete connectors in prefabricated steel–concrete composite beams

Analysis on the potential of Pennisetum hydridum for phytoremediation of Cd-polluted soil fertilized by worm castings

Soil heavy metal pollution including Cd, is the main factor that causes the decline of ecological environment quality, the excessive content in crops and the harm to human health. Phytoremediation is one of the important ways to control heavy metals, which has both ecological and economic benefits. However, most plant species have limited remediation ability and cannot achieve good heavy metal removal effect. In contrast, P. hydridum, easy to cultivate, has large biomass and short growth cycle, shows strong restoration ability in the treatment of heavy metal polluted soil. In order to explore its phytoremediation in Cd-polluted soils under appropriate agronomic measures, this experiment adopts the field random block experiment design to study the control effect and application safety of the application of organic fertilizers (warm castings and biogas slurry) to plant it in the Cd-polluted farmland. The results showed the Cd in the soil after P. hydridum harvesting was 0.53–0.56 mg/kg, and the partial Cd in the shoot was 0.21–0.28 mg/kg (fresh weight), and the enrichment coefficients were all greater than 1, and the extraction amount and efficiency of Cd were 7.17–9.43 mg/m2 and 5.71%–7.01%, respectively. All those data express a decrease in Cd under various treatment conditions, indicating that, P. hydridum can grow under high concentration and it has a certain enrichment effect on Cd, especially in the application of organic fertilizers, which could not only improve the growth performance of the plant, but also improve the soil, much better than that of other Cd hyper-accumulators. Moreover, the positive correlation between the biomass allocation rate and Cd in the soil reflects that the biomass allocation of the plant behaved in different ways with the increase of Cd oil. It is also feasible in terms of application safety due to a long and gradual process to enrich Cd in soil. This study made a proof that it would be a green and environmentally friendly treatment method by making good use of its high biomass to adsorb and remove heavy metals from soil, which would have a good application prospect and development value.

Mechanistic insights into the P-coumaric acid protection against bisphenol A-induced hepatotoxicity in in vivo and in silico models

Evaluation of statistical methods applied in theses and dissertations in an Open, Distance and e-Learning University

The appropriate application of research methods and statistical analyses used in the studies directly affects the quality of scientific studies. Due to the possibility of employing an incorrect statistical technique, it is crucial to choose a statistical method based on the study’s data and research objectives. This study aimed to evaluate whether statistical techniques applied in the theses and dissertations were appropriate for planning surveys or experiments and analyzing data, and to identify common mistakes that master’s and doctoral students made when using statistical techniques for the intended goals. The study reviewed 139 master’s theses and doctoral dissertations submitted to seven agricultural and environmental sciences disciplines at a leading Open, Distance and e-learning university in Africa between 2015 and 2020. These dissertations and theses used mixed and quantitative research methods. The analysis of variance test was the most often used statistical test, according to the results, followed by the student t-test and the Chi-square test. At least one blatant methodological error was found in 41.0% of theses and dissertations, either in the data collection process or in the data analysis. Examples of these errors include the use of a simple random sampling technique despite the heterogeneous population units, the conversion of count responses to binary responses and percentages for fitting logistic and general binomial regression models, and the incorrect modeling of correlated data using generalized linear models. The results of this study will create greater awareness of the common errors that postgraduate students make when using statistical methods to design experiments or sample surveys and analyse data. In addition, the findings inform the university management to plan for specific training in statistical methods appropriate for a range of academic fields.

Ultrasound-based incidence of coarctation of the aorta in true and false positive fetuses

Editorial Note: Prolonged immune alteration following resolution of acute inflammation in humans

Paired proteomic analysis reveals protein alterations in sun-exposed skin of professional drivers

Abstract Professional drivers represent an ideal cohort for investigating the effects of solar radiation on skin due to their unique, asymmetric exposure to sun, a consequence of vehicle window orientations. Consequently, one side of the face is naturally subjected to more solar radiation, resulting in uneven sunlight exposure. This scenario supports a paired experimental design for precise within-individual comparisons, crucial for assessing sun exposure’s impact on skin health, including signs of aging. Leveraging this approach, our study reveals sun-induced overexpression of proteins linked to photoaging through paired proteomic analysis, providing novel insights into the skin’s adaptive responses to chronic solar exposure. Initially, our research focused on a dataset from ten male professional drivers, identifying a set upregulated proteins in sun-exposed skin compared to the less exposed side of the face. To validate these findings, we extended our investigation to a new cohort of seven female bus drivers. Our motivation in switching genders and utilizing different mass spectrometry equipment and sample preparation techniques was for assessing the robustness of our initial findings, encompassing not just sex differences but also methodological variations, and also for understanding the broader implications of our results for photodermatology. To enable this detailed analysis, we developed specialized software that allows precise paired proteomic analysis, significantly enhancing the robustness and clarity of our findings. Our results shortlisted keratins, S100A14, and F-box proteins—by remaining consistently overexpressed in sun-exposed skin—and hemoglobin subunit beta as downregulated across both cohorts. Our findings underscore the potential of proteomic techniques in advancing our understanding of the molecular dynamics of photoaging and highlight the value of selecting cohorts with specific exposure characteristics.

Ictal cardiovascular autonomic dysfunction during focal seizures induced by direct electrical stimulation: An observational study research protocol

Introduction Autonomic symptoms, such as changes in heart rate, blood pressure, or respiration often accompany epileptic seizures and, in some cases, may be life threatening or even contribute to sudden death. However, autonomic changes during seizures with onset from certain brain areas are insufficiently understood. Intracranial direct electrical stimulation during stereoelectroencephalographic (SEEG) monitoring in surgical candidates allows researchers to investigate autonomic responses to induced seizures in conscious patients with known precise location of the electrodes. We aimed to identify the epileptogenic focus locations or brain structures associated with ictal cardiovascular autonomic dysfunction during focal seizures induced by direct electrical stimulation. Methods and analysis This is an observational study. In focal epilepsy patients undergoing presurgical evaluation with implanted intracranial SEEG electrodes, we will record heart rate (HR), beat-to-beat blood pressure (BP), and respiratory rate during the SEEG monitoring and stimulation conducted in accordance with the clinical needs. Tachycardia (HR > 100 bpm), bradycardia (HR < 60 bpm), hypertension (systolic or diastolic BP ≥ 140/90 mmHg), and hypotension (systolic or diastolic BP < 90/60 mmHg) during the first minute of induced clinical seizures will be considered as ictal cardiovascular autonomic dysfunction. We will use the chi-squared test to compare percentage of dysautonomia-associated seizures in the total number of induced seizures between cortical areas related to or interconnected with the central autonomic network and other cortical areas. Significance will be assumed for p-values < 0.05. At the time of submission, this study has enrolled thirteen patients and still on-going.