Search Results (61)

This study presents PolypeptideDesigner (PPD), a novel conditional diffusion-based model for de novo polypeptide sequence design and generation based on per-residue secondary structure conditions. By integrating a lightweight LSTM-attention neural network as the denoiser within a diffusion framework, PPD offers an innovative and efficient approach to polypeptide generation. Evaluations demonstrate that the PPD model can generate diverse and novel polypeptide sequences across various testing conditions, achieving high pLDDT scores when folded by ESMFold. In comparison to the ProteinDiffusionGenerator B (PDG-B) model, a relevant benchmark in the field, PPD exhibits the ability to produce longer and more diverse polypeptide sequences. This improvement is attributed to PPD’s optimized architecture and expanded training dataset, which enhance its understanding of protein structural pattern. The PPD model shows significant potential for optimizing functional polypeptides with known structures, paving the way for advancements in biomaterial design. Future work will focus on further refining the model and exploring its broader applications in polypeptide engineering. Full article

Background/Objectives: Several gene targets were identified for psoriasis. Some are currently being explored as potential therapeutic targets, including CCL11. Our task was to prove a possible association of single-nucleotide polymorphisms +67 G/A and -426 T/C in the eotaxin gene (CCL11, 17q 21.3) with the development and clinical aspects of psoriasis as an immune-based dermatological disease and evaluate its relationship to potential comorbidities. Material and Methods: In total, 460 patients with psoriasis were included in the case–control and genotype–phenotype study together with 167 control persons of similar age and sex distributions without a personal and/or family history of chronic disease of the skin. Two eotaxin gene polymorphisms were detected from isolated DNA via standard PCR, restriction analysis methods, and horizontal electrophoresis. Results: No significant case–control differences in the frequency of the CCL11 genotype in both polymorphisms were observed. In polymorphism +67 G/A, a significant increase in the AA genotype in patients with psoriasis guttata compared to plaque psoriasis was found (p = 0.006). A significant association of the A allele in psoriatic patients with a personal history of allergy was found (p = 0.02). The A alle was also significantly associated with a family history of psoriasis (p = 0.00008). In men, a higher risk of a delayed start of psoriasis (later than 40 years) associated with the T allele of -426 T/C polymorphism (p = 0.0007) was found. When double genotypes of both polymorphisms were evaluated, we observed significant differences in double genotype distribution between men with and without a family history of allergy (Pdg = 0.0005) and between those with and without affected siblings (Pdg = 0.03). In women with psoriasis, a higher risk of the TT genotype of -426 T/C polymorphism in patients with a personal history of diabetes (p = 0.001) as well as in patients with both a personal history of cardiovascular disease and diabetes (p = 0.00005) was proved. When double genotypes of both polymorphisms were evaluated, the significance of double genotype difference between those with and without personal history of diabetes was very high (Pdg = 0.0002). Similarly, the significance of the double genotype difference between those with and without personal history of cardiovascular diseases and diabetes was very high (Pdg = 0.000001). Conclusions: CCL11 is considered one of the basic chemokines responsible for the origin and development of immune-based reactions. Based on our results, we suggest that the +67 G/A CCL11 polymorphism should be considered as a gene modulator of psoriasis in specific subgroups of patients. Full article

A new method of producing metal powders for additive manufacturing by the atomization of free-falling melt streams using pulsed cross-flow gaseous shock or detonation waves is proposed. The method allows the control of shock/detonation wave intensity (from Mach number 4 to about 7), as well as the composition and temperature of the detonation products by choosing proper fuels and oxidizers. The method is implemented in laboratory and industrial setups and preliminarily tested for melts of three materials, namely zinc, aluminum alloy AlMg5, and stainless steel AISI 304, possessing significantly different properties in terms of density, surface tension, and viscosity. Pulsed shock and detonation waves used for the atomization of free-falling melt streams are generated by the pulsed detonation gun (PDG) operating on the stoichiometric mixture of liquid hydrocarbon fuel and gaseous oxygen. The analysis of solidified particles and particle size distribution in the powder is studied by sifting on sieves, optical microscopy, laser diffraction wet dispersion method (WDM), and atomic force microscopy (AFM). The operation process is visualized by a video camera. The minimal size of the powders obtained by the method is shown to be as low as 0.1 to 1 μm, while the maximum size of particles exceeds 400–800 μm. The latter is explained by the deficit of energy in the shock-induced cross-flow for the complete atomization of the melt stream, in particular dense and thick (8 mm) streams of the stainless-steel melt. The mass share of particles with a fraction of 0–10 μm can be at least 20%. The shape of the particles of the finest fractions (0–30 and 30–70 μm) is close to spherical (zinc, aluminum) or perfectly spherical (stainless steel). The shape of particles of coarser fractions (70–140 μm and larger) is more irregular. Zinc and aluminum powders contain agglomerates in the form of particles with fine satellites. The content of agglomerates in stainless-steel powders is very low. In general, the preliminary experiments show that the proposed method for the production of finely dispersed metal powders demonstrates potential in terms of powder characteristics. Full article

Protected areas (PAs) are geographical spaces intended to conserve populations, communities, and ecosystems, in which species richness must be maximized, the conserved area must be minimized, and anthropogenic pressure must be reduced. The present study analyzed the representativeness, complementarity, and degree of risk of 25 garter snake species of the genus Thamnophis in the PAs of Mexico. This study proposes that at least 17% of the potential geographic distribution (PGD) of species will be found inside PAs and in areas (Aichi Target 11) with a low human footprint (HF). The PGD of species was associated with the PAs and HF layers to identify where and which species could be at local extirpation risk by human activities. The results indicate that the federal PAs contain 85.2% of the species, while the state PAs contain 77.7% of the species. An average of 13.4% of the PGD of these species is found inside PAs, and two species are found outside. In 13 federal PAs and 10 state PAs, the Thamnophis species present high local extirpation risk from human activities. In total, 37% of species are found in PAs with a medium to very high human footprint; therefore, their persistence could be at local extirpation risk. Compared to other taxa, species of the genus Thamnophis are well represented. However, the PDG of more than half of the species achieves Aichi Target 11. Full article

Activated carbon is widely known for its porous structure and diverse surface functional groups, making it an effective adsorbent for removing various organic and inorganic pollutants from air and water. However, as a filtration material in air conditioning systems, activated carbon can also provide favorable conditions for microbial growth, potentially leading to the proliferation of microorganisms on its surface. These microorganisms, along with their metabolic products, can be released into indoor environments, posing potential health risks. This study employs molecular simulation to investigate the adsorption and release mechanisms of microorganisms and their volatile organic compound (VOC) metabolic products on activated carbon. Peptidoglycan (PDG) (as a representative bacterial cell wall component) and p-xylene (as a representative microbial metabolic product) were used as model compounds. The adsorption behavior of these compounds was simulated on activated carbon under different environmental conditions, including varying temperatures. The study found that activated carbon has a higher affinity for peptidoglycan than for p-xylene; at 303.15 K, the diffusion coefficients of peptidoglycan and p-xylene in activated carbon are 0.842 × 10⁻⁹ m²/s and 0.587 × 10⁻⁸ m²/s, respectively. Temperature plays an important role in affecting adsorption capacity; when the temperature rises by 10 K, the diffusion coefficients of peptidoglycan and p-xylene in activated carbon increase by 32.8% and 34.3%, respectively. These insights contribute to the development of efficient and health-conscious air purification materials, offering theoretical and practical guidance for optimizing the use of activated carbon in HVAC systems. Full article

Treatment options for pulmonary arterial hypertension (PAH) have improved substantially in the last 30 years, but there is still a need for novel molecules that can regulate the excessive accumulation of pulmonary artery smooth muscle cells (PASMCs) and consequent vascular remodeling. One set of possible candidates are protein kinases. The study provides an overview of existing preclinical and clinical data regarding small-molecule protein kinase inhibitors in PAH. Online databases were searched from 2001 to 2023 according to PRISMA. The corpus included preclinical studies demonstrating alterations in at least one PH-related parameter following chronic exposure to an individual protein kinase inhibitor, as well as prospective clinical reports including healthy adults or those with PAH, with primary outcomes defined as safety or efficacy of an individual small-molecule protein kinase inhibitor. Several models in preclinical protocols (93 papers) have been proposed for studying small-molecule protein kinase inhibitors in PAH. In total, 51 kinase inhibitors were tested. Meta-analysis of preclinical results demonstrated seralutinib, sorafenib, fasudil hydrochloride, and imatinib had the most comprehensive effects on PH with anti-inflammatory, anti-oxidant, and anti-proliferative potential. Fasudil demonstrated more than 70% animal survival with the longest experimental period, while dasatinib, nintedanib, and (R)-crizotinib could deteriorate PAH. The substances targeting the same kinases often varied considerably in their activity, and such heterogeneity may be due to the variety of causes. Recent studies have addressed the molecules that affect multiple networks such as PDG-FRα/β/CSF1R/c-KIT/BMPR2 or FKBP12/mTOR. They also focus on achieving a satisfactory safety profile using innovative inhalation formulations Many small-molecule protein kinase inhibitors are able to control migration, proliferation and survival in PASMCs in preclinical observations. Standardized animal models can successfully reduce inter-study heterogeneity and thereby facilitate successful identification of candidate drugs for further evaluations. Full article

The aquatic γ-proteobacterium Shewanella oneidensis is able to form two types of biofilms: a floating biofilm at the air–liquid interface (pellicle) and a solid surface-associated biofilm (SSA-biofilm). S. oneidensis possesses the Bpf system, which is orthologous to the Lap system first described in Pseudomonas fluorescens. In the Lap systems, the retention of a large adhesin (LapA) at the cell surface is controlled by LapD, a c-di-GMP effector protein, and LapG, a periplasmic protease targeting LapA. Here, we showed that the Bpf system is mandatory for pellicle biogenesis, but not for SSA-biofilm formation, indicating that the role of Bpf is somewhat different from that of Lap. The BpfD protein was then proved to bind c-di-GMP via its degenerated EAL domain, thus acting as a c-di-GMP effector protein like its counterpart LapD. In accordance with its key role in pellicle formation, BpfD was found to interact with two diguanylate cyclases, PdgA and PdgB, previously identified as involved in pellicle formation. Finally, BpfD was shown to interact with CheY3, the response regulator controlling both chemotaxis and biofilm formation. Altogether, these results indicate that biofilm formation in S. oneidensis is under the control of a large c-di-GMP network. Full article

Background and Objectives: Fertility tracking apps and devices are now currently available, but urinary hormone levels lack accuracy and sensitivity in timing the start of the 6-day fertile window and the precise 24 h interval of transition from ovulation to the luteal phase. We hypothesized the serum hormones estradiol (E2) and progesterone (P) might be better biomarkers for these major ovulatory cycle events, using appropriate mathematical tools. Materials and Methods: Four women provided daily blood samples for serum E2, P, and LH (luteinizing hormone) levels throughout their entire ovulatory cycles, which were indexed to the first day of dominant follicle (DF) collapse (defined as Day 0) determined by transvaginal sonography; therefore, ovulation occurred in the 24 h interval of Day −1 (last day of maximum diameter DF) to Day 0. For comparison, a Mira^TM fertility monitor was used to measure daily morning urinary LH (ULH), estrone-3-glucuronide (E3G), and pregnanediol-3-glucuronide (PDG) levels in three of these cycles. Results: There were more fluctuations in the Mira^TM hormone levels compared to the serum levels. Previously described methods, the Fertility Indicator Equation (FIE) and Area Under the Curve (AUC) algorithm, were tested for identifying the start of the fertile window and the ovulation/luteal transition point using the day-specific hormone levels. The FIE with E2 levels predicted the start of the 6-day fertile window on Day −7 (two cycles) and Day −5 (two cycles), whereas no identifying signal was found with E3G. However, both pairs of (E2, P) and (E3G, PDG) levels with the AUC algorithm signaled the Day −1 to Day 0 ovulation/luteal transition interval in all cycles. Conclusions: serum E2 and (E2, P) were better biomarkers for signaling the start of the 6-day fertile window, but both Mira^TM and serum hormone levels were successful in timing the [Day −1, Day 0] ovulatory/luteal transition interval. These results can presently be applied to urinary hormone monitors for fertility tracking and have implications for the direction of future fertility tracking technology. Full article

In the past, during development processes, major ecological and environmental problems have occurred in the agro-pastoral ecotone of China, which have had a strong impact on regional sustainable development. As such, analyzing the evolution of the regional ecosystem service value (ESV) and predicting the futural spatio-temporal evolution under different development scenarios will provide a scientific basis for further sustainable development. This research analyzed the regional land use and land cover change (LUCC) from 2000 to 2020, adopted the Mark-PLUS model to construct different scenarios (prioritizing grassland development, PDG; prioritizing cropland development, PCD; business as usual, BAU), and simulated the future LUCC. The driving factors influencing each land use type were revealed using the PLUS model. Based on the LUCC data, the spatio-temporal distribution of the regional ESV was calculated via the ESV equivalent factor method, including four primary services (supply service, adjustment service, support service, and cultural service) and eleven secondary services (water resource supply, maintaining nutrient circulation, raw material production, aesthetic landscape, food production, environmental purification, soil conservation, maintaining biodiversity, gas regulation, climate regulation, and hydrologic regulation). The results showed that the total ESV increased first and then declined from 2000 to 2020, reaching the highest value of CNY 8207.99 million in 2005. In the different future scenarios, the ESV shows a trend of PGD (CNY 8338.79 million) > BAU (CNY 8194.82 million) > PCD (CNY 8131.10 million). The global Moran index also follows this distribution. Additionally, precipitation (18%), NDVI (16%), and DEM (16%) are the most important factors in the regional LUCC. The spatial agglomeration characteristics of ESV were revealed using the global Moran’s index and local indicators of spatial auto-correlation, which show a high coordination degree between the high–high cluster areas and water areas. These results point out the key points in the next step of ecological restoration projects and help with achieving the sustainable development goals more effectively. Full article

The mass spectrum of different meson particles is generated using an effective Lagrangian of the extended linear-sigma model (eLSM) for scalar and pseudoscalar meson fields and quark flavors, up, down, strange, and charm. Analytical formulas for the masses of scalar, pseudoscalar, vector, and axialvector meson states are derived assuming global chiral symmetry. The various eLSM parameters are analytically deduced and numerically computed. This enables accurate estimations of the masses of sixteen noncharmed and thirteen charmed meson states at vanishing temperature. The comparison of these results to a recent compilation of the particle data group (PDG) allows us to draw the conclusion that the masses of sixteen noncharmed and thirteen charmed meson states calculated in the eLSM are in good agreement with the PDG. This shows that the eLSM, with its configurations and parameters, is an effective theoretical framework for determining the mass spectra of various noncharmed and charmed meson states, particularly at vanishing temperature. Full article

The thermodynamic modeling of waste oil (WO) gasification by a high-temperature gasification agent (GA) composed of an ultra-superheated H₂O/CO₂ mixture is carried out. The GA is assumed to be obtained by the gaseous detonation of fuel–oxidizer–diluent mixture in a pulsed detonation gun (PDG). N-hexadecane is used as a WO surrogate. Methane or the produced syngas (generally a mixture of H₂, CO, CH₄, CO₂, etc.) is used as fuel for the PDG. Oxygen, air, or oxygen-enriched air are used as oxidizers for the PDG. Low-temperature steam is used as a diluent gas. The gasification process is assumed to proceed in a flow-through gasifier at atmospheric pressure. It is shown that the use of the detonation products of the stoichiometric methane–oxygen and methane–air mixtures theoretically leads to the complete conversion of WO into a syngas consisting exclusively of H₂ and CO, or into energy gas with high contents of CH₄ and C₂-C₃ hydrocarbons and an LHV of 36.7 (fuel–oxygen mixture) and 13.6 MJ/kg (fuel–air mixture). The use of the detonation products of the stoichiometric mixture of the produced syngas with oxygen or with oxygen-enriched air also allows theoretically achieving the complete conversion of WO into syngas consisting exclusively of H₂ and CO. About 33% of the produced syngas mixed with oxygen can be theoretically used for PDG self-feeding, thus making the gasification technology very attractive and cost-effective. To self-feed the PDG with the mixture of the produced syngas with air, it is necessary to increase the backpressure in the gasifier and/or enrich the air with oxygen. The addition of low-temperature steam to the fuel–oxygen mixture in the PDG allows controlling the H₂/CO ratio in the produced syngas from 1.3 to 3.4. Full article

Printed circuit boards (PCBs) are the main components of e-waste. In order to reduce the negative impact of waste PCBs on human health and the environment, they must be properly disposed of. A new method is demonstrated for recycling waste PCBs. It is referred to as the high-temperature thermo-mechano-chemical gasification (TMCG) of PCBs by the detonation-born gasification agent (GA), which is a blend of H₂O and CO₂ heated to a temperature above 2000 °C. The GA is produced in a pulsed detonation gun (PDG) operating on a near-stoichiometric methane–oxygen mixture. The PDG operates in a pulsed mode producing pulsed supersonic jets of GA and pulsed shock waves possessing a huge destructive power. When the PDG is attached to a compact flow reactor filled with waste PCBs, the PCBs are subject to the intense thermo-mechano-chemical action of both strong shock waves and high-temperature supersonic jets of GA in powerful vortical structures established in the flow reactor. The shock waves grind waste PCBs into fine particles, which undergo repeated involvement and gasification in the high-temperature vortical structures of the GA. Demonstration experiments show full (above 98%) gasification of the 1 kg batch of organic matter in a setup operation time of less than 350 s. The gaseous products of PCB gasification are mainly composed of CO₂, CO, H₂, N₂, and CH₄, with the share of flammable gas components reaching about 45 vol%. The solid residues appear in the form of fine powder with visible metal inclusions of different sizes. All particles in the powder freed from the visible metal inclusions possess a size less than 300–400 μm, including a large fraction of sizes less than 100 μm. The powder contains Sn, Pb, Cu, Ni, Fe, In, Cd, Zn, Ca, Si, Al, Ti, Ni, and Cl. Among these substances, Sn (10–20 wt%), Pb (5–10 wt%), and Cu (up to 1.5 wt%) are detected in the maximum amounts. In the powder submitted for analysis, precious elements Ag, Au, and Pt are not detected. Some solid mass (about 20 wt% of the processed PCBs) is removed from the flow reactor with the escaping gas and is partly (about 10 wt%) trapped by the cyclones in the exhaust cleaning system. Metal inclusions of all visible sizes accumulate only in the flow reactor and are not detected in powder samples extracted from the cyclones. The gasification degree of the solid residues extracted from the cyclones ranges from 76 to 91 wt%, i.e., they are gasified only partly. This problem will be eliminated in future work. Full article

Bacillus subtilis, a probiotic bacterium with engineering potential, is widely used for the expression of exogenous proteins. In this study, we utilized the integrative plasmid pDG364 to integrate the hemagglutinin–neuraminidase (HN) gene from Newcastle disease virus (NDV) into the genome of the B. subtilis 168 model strain. We successfully constructed a recombinant B. subtilis strain (designated B. subtilis RH) that displays a truncated HN antigen fragment on the surface of its spores and further evaluated its immunogenic effects in mice. Using ELISA, we quantified the levels of IgG in serum and secretory IgA (sIgA) in intestinal contents. The results revealed that the recombinant B. subtilis RH elicited robust specific mucosal and humoral immune responses in mice. Furthermore, B. subtilis RH demonstrated potential mucosal immune adjuvant properties by fostering the development of immune organs and augmenting the number of lymphocytes in the small intestinal villi. Additionally, the strain significantly upregulated the relative expression of inflammatory cytokines such as IL-1β, IL-6, IL-10, TNF-α, and IFN-γ in the small intestinal mucosa. In conclusion, the B. subtilis RH strain developed in this study exhibits promising mucosal immunogenic effects. It holds potential as a candidate for an anti-NDV mucosal subunit vaccine and offers a novel preventive strategy for the poultry industry against this disease. Full article

The rise of graph neural networks has greatly contributed to the development of recommendation systems, and self-supervised learning has emerged as one of the most important approaches to address sparse interaction data. However, existing methods mostly focus on the recommendation’s accuracy while neglecting the role of recommended item diversity in enhancing user interest and merchant benefits. The reason for this phenomenon is mainly due to the bias of popular items, which makes the long-tail items (account for a large proportion) be neglected. How to mitigate the bias caused by item popularity has become one of the hot topics in current research. To address the above problems, we propose a Popularity-Debiased Graph Self-Supervised for Recommendation (PDGS). Specifically, we apply a penalty constraint on item popularity during the data enhancement process on the user–item interaction graph to eliminate the inherent popularity bias. We generate item similarity graphs with the popularity bias removed to construct a self-supervised learning task under multiple views, and we design model optimization strategies from the perspectives of popular items and long-tail items to generate recommendation lists. We conduct a large number of comparison experiments, as well as ablation experiments, on three public datasets to verify the effectiveness and the superiority of the model in balancing recommendation accuracy and diversity. Full article

Gravity on Earth is of great interest in geodesy, geophysics, and natural resource exploration. Ship-based gravimeters are a widely used instrument for the collection of surface gravity field data in marine regions. However, due to the considerable distance from the sea surface to the seafloor, the spatial resolution of surface gravity data collected from ships is often insufficient to image the detail of seafloor geological structures and to explore offshore natural minerals. Therefore, the development of a mobile underwater gravimetry system is necessary. The GraviMob gravimeter, developed for a moving underwater platform by Geo-Ocean (UMR 6538 CNRS-Ifremer-UBO-UBS), GeF (UR4630, Cnam) and MAPPEM Geophysics, has been tested over the last few years. In this study, we report on the high-resolution gravity measurements from the GraviMob system mounted on an Autonomous Underwater Vehicle, which can measure at depths of up to several kilometres. The dedicated GraviMob underwater gravity measurements were conducted in the Mediterranean Sea in March 2016, with a total of 26 underwater measurement profiles. All these measurement profiles were processed and validated. In a first step, the GraviMob gravity measurements were corrected for temperature based on a linear relationship between temperature and gravity differences. Through repeated profiles, we acquired GraviMob gravity measurements with an estimated error varying from 0.8 to 2.6 mGal with standard deviation after applying the proposed temperature correction. In a second step, the shipborne gravity data were downward continued to the measurement depth to validate the GraviMob measurements. Comparisons between the corrected GraviMob gravity anomalies and downward continued surface shipborne gravity data revealed a standard deviation varying from 0.8 to 3.2 mGal and a mean bias value varying from −0.6 to 0.6 mGal. These results highlight the great potential of the GraviMob system in measuring underwater gravity. Full article