Search Results (88)

Grant-free non-orthogonal multiple access (NOMA) enables communication without a scheduling process. Base station (BS) must detect active users without knowing their number, a challenge that also occurs in grant-free NOMA–Internet of Things (IoT). Device detection in grant-free NOMA-IoT can be considered as signal reconstruction in compressive sensing (CS). To address this limitation, we propose extended sparsity estimation- orthogonal matching pursuit (ESE-OMP) to detect active devices in single measurement vector (SMV) and multiple measurement vector (MMV) problems for grant-free NOMA-IoT systems, a reconstruction method in CS that operates without prior knowledge of the sparsity level, which corresponds to the number of active devices. The algorithm iteratively detects active devices by monitoring the absolute difference in $l_1$-norm of successive residuals, terminating when the change falls below a predefined threshold $\epsilon$. ESE-OMP is evaluated under various grant-free NOMA-IoT systems, irregular low-density spreading-orthogonal frequency division multiplexing (LDS-OFDM), regular LDS-OFDM, and pattern division multiple access (PDMA) systems. When the signal-to-noise ratio (SNR) is 10 dB for the SMV problem with static active device composition, the regular LDS-OFDM system achieves a bit error rate (BER) of $2.95\times {10}^{-4}$, while irregular LDS-OFDM and PDMA systems achieve BERs of $3.78\times {10}^{-3}$ and $1.79\times {10}^{-2}$, respectively. The smaller the number of active devices, the better the performance of ESE-OMP. Full article

Background/Objectives: Antimicrobial resistance (AMR) in Escherichia coli is a growing public health concern, particularly in regions affected by environmental contamination and poor wastewater management. Data on locally isolated E. coli-targeting phages in Lebanon remain limited. This study aimed to isolate, characterize, and evaluate two lytic bacteriophages against AMR E. coli. Methods: Two phages, EPIMAM01 (gb:PQ493298) and EPIMRB01 (gb:PQ657784), were isolated from untreated sewage in Beirut using E. coli ATCC 25922. Characterization included double-layer agar assays, one-step growth analysis, and stability testing across temperature and pH ranges. Bacteriolytic activity was assessed in planktonic cultures and preformed biofilms. Host range and efficiency of plating (EOP) were evaluated using clinical isolates. Whole-genome sequencing and comparative analyses were performed. Results: Both phages produced clear plaques and showed a latent period of ~40 min. EPIMAM01 had a higher estimated burst size (140 PFU/infected cell) than EPIMRB01 (75 PFU/infected cell). Both phages remained stable between 4–50 °C and within a pH range of 5–10 but showed marked loss of activity at temperatures ≥60 °C and pH ≤3 or ≥12. EPIMAM01 effectively inhibited planktonic growth of E. coli ATCC 25922, whereas EPIMRB01 showed stronger biofilm-disrupting activity against preformed E. coli biofilms. Both phages lysed several of the 17 tested clinical E. coli isolates. Comparative analyses of gene presence/absence patterns, bacterial defense systems, and adsorption phenotypes among the tested E. coli strains identified mlaA, ydcQ, and ompD-2 as candidate adsorption-associated genes and suggested CRISPR systems may reduce susceptibility. Genomic analysis classified both phages as T4-like phages lacking lysogeny, virulence, or AMR genes. Conclusions: EPIMAM01 and EPIMRB01 are lytic phages with complementary antimicrobial properties, supporting their potential for further development as AMR control agents. Full article

Background/Objectives: Escherichia coli (E. coli) spans commensal, intestinal pathogenic, and extraintestinal pathogenic lineages distributed across human, animal, and environmental reservoirs, yet the extent to which virulence architectures are shared across these compartments remains incompletely understood. Using a One Health framework, we profiled putative virulence determinants in pooled multidrug-resistant (MDR) E. coli source groups representing human, animal, and environmental sectors. Methods: Virulence genes were predicted with VirulenceFinder, and presence–absence profiles were integrated to define functional composition, sector overlap, source-group distribution breadth, and pathotype-associated signatures. Predicted pathogenic potential was assessed with PathogenFinder and compared with pathogenic family richness. Results: Overall, 114 putative virulence genes were detected, with adhesion/colonization functions dominating the virulome (33/114), followed by toxin-associated genes (12/114). A conserved core of 50 virulence genes was shared across all three sectors, including determinants linked to serum resistance (iss, ompT, traT), adhesion (csgA, fimH), stress adaptation (terC), and iron acquisition (sitA, iutA, fyuA). ExPEC-associated determinants were most numerous in environmental source groups (n = 52), whereas diarrheagenic E. coli markers were most frequent in animal-associated groups (n = 42). LEE-associated effectors were infrequent and largely absent from human source groups. Despite ecological differences in virulence composition, pathogenicity scores remained consistently high across sectors (0.83–0.92) and showed no significant association with pathogenic family richness (Spearman’s ρ = 0.197, p = 0.392). Conclusions: Within the limits of pooled source-group analysis, these findings suggest that MDR E. coli across One Health compartments shares a broadly distributed, ExPEC-associated virulence repertoire overlaid with sector-specific pathotype signals, underscoring the value of integrated genomic surveillance while highlighting the need for isolate-resolved analysis. Full article

Background/Objectives: Extraintestinal pathogenic Escherichia coli (ExPEC) is a major pathogen that causes septicemia, meningitis, and polyserositis in pigs. The increasing prevalence of antimicrobial resistance and the diverse serotypes of ExPEC highlight the urgent need for broadly protective vaccines. Methods and Results: In this study, an OmpC epitope vaccine based on the T4 phage display system was developed and evaluated. Two B-cell epitopes (OmpC-1 and OmpC-2) were identified by bioinformatic analysis and displayed on recombinant T4 phages. Immunization induced strong antigen-specific IgG responses, with the OmpC-1-T4 group showing significantly higher antibody titers than the OmpC protein group. In the O11 serotype PCN033 challenge model, survival rates reached 100% in the OmpC-1-T4 group, 60% in the OmpC-2-T4 group, and approximately 80% in the OmpC protein group. In the O18 serotype 2103 challenge model, both recombinant phage groups had survival rates of approximately 60%, whereas all the mice in the OmpC protein group died within three days. OmpC-1-T4 immunization also significantly reduced bacterial loads in lung and brain tissues after PCN033 infection and decreased TNF-α and IL-6 expression in lung tissues, accompanied by reduced inflammatory infiltration and tissue damage. Conclusions: Overall, the T4 phage-displayed OmpC epitope vaccine induced strong humoral immunity and provided protection against different ExPEC serotypes. Among the candidates, OmpC-1-T4 showed superior immune protection, bacterial clearance, and inflammation control, supporting its potential as a vaccine candidate against porcine ExPEC infection. Full article

Fully polarimetric SAR provides richer scattering information than single-polarisation imaging, but multichannel sparse image formation can be computationally and memory demanding, especially when channels are processed jointly. In our previous work, we introduced Orthogonal Matching Pursuit 2D Fully Polarimetric (OMP2D-FP), a greedy reconstruction algorithm that enforces a shared spatial support across polarimetric channels while exploiting a separable 2D formulation to avoid vectorisation and reduce computational burden and memory footprint relative to vectorised OMP-based formulations. In this paper, we extend its validation to real measurements and further develop its theoretical foundations by recasting the atom-selection step as a detection–estimation problem, thereby defining a cumulative objective function (COF) design space that enables the incorporation of disturbance statistics and prior knowledge into sparse recovery. Experiments on fully polarimetric SAR data of a T-72 tank over a wide range of aspect angles, SNR levels, and measurement percentages show that joint support selection improves reconstruction fidelity and polarimetric information preservation over independent per-channel processing, with particularly clear gains under challenging conditions. Preliminary applications of the COF framework (a whitening COF incorporating polarimetric clutter statistics and a mask-based COF incorporating spatial prior knowledge) yield encouraging results, motivating further systematic investigation of adaptive COF designs. Full article

Antimicrobial resistance has renewed interest in bacteriophage therapy, yet bacterial evolution frequently undermines treatment efficacy. Combination phage therapy is commonly implemented as simultaneous phage cocktails, but whether this is optimal remains in question. Here, we experimentally compared simultaneous versus sequential administration of two phages, an evolved λ called ‘λtrn’ and T2, on Escherichia coli K-12 under controlled laboratory conditions. Across replicated experiments, treatment outcome depended strongly on delivery strategy, dosing order, and timing. Contrary to expectations, sequential delivery consistently achieved greater and more sustained bacterial suppression than simultaneous cocktails, although only when T2 initiated the sequence. Phenotypic assays revealed that treatment differences were driven by the accessibility and timing of cross-resistance evolution. λ-first treatments rapidly selected for cross-resistant bacteria prior to exposure to the second phage, rendering subsequent treatment ineffective. In contrast, T2-first sequential treatments delayed or limited cross-resistance and frequently produced single-phage resistance or collateral sensitivity. Cocktail treatments showed intermediate dynamics, with cross-resistance evolving more slowly but consistently. Whole genome sequencing identified distinct genetic routes to cross-resistance, including regulatory mutations in envZ affecting expression of the phage receptor OmpF, as well as envelope-modifying, mucoidy-associated mutations. Engineering envZ mutations into unevolved backgrounds confirmed the mutation’s sufficiency to confer low-cost cross-resistance. Together, these results demonstrated that phage therapy efficacy depended not only on phage composition but on how selection pressures were ordered in time, highlighting evolutionary steering as a powerful principle for multi-phage therapy design. Full article

This study aimed to design a multi-epitope vaccine (MEV) against Pasteurella multocida (Pm) using immunoinformatics approaches. Based on four conserved outer membrane proteins (OmpA; OmpH; PlpEand LolA), 15 immunodominant epitopes were identified, including 8 CTL epitopes, 3 HTL epitopes, and 4 B-cell epitopes. A vaccine construct was developed by incorporating RGD and PADRE adjuvant sequences. Computational analyses indicated that the vaccine possesses favorable physicochemical properties and structural stability. The molecular docking and normal mode analyses reveal a potential binding interface between the basis and TLR2/TLR4, with a computed binding energy of −10.1 kcal/mol for TLR4, suggesting a possible preferential interaction. Immune simulation predicted the vaccine could effectively elicit responses from B cells, T cells, and key cytokines such as IFN-γ. Additionally, the vaccine sequence was successfully cloned into the pET-28a (+) expression vector, facilitating future recombinant expression. This study provides a theoretical foundation for developing a safe and effective subunit vaccine against Pm. Full article

Background: Brucella outer membrane proteins (Omps) are an important part of its cell wall and major virulence-related factors. Omp16 and Omp19 proteins are the advantageous antigens of Brucella and have been widely used in research on vaccines against brucellosis. As an emerging vaccine, the mRNA vaccine has unique advantages in the fight against intracellular parasitic bacteria. Methods: In this study, mRNA encoding the omp16 and omp19 genes of Brucella. melitensis (B. melitensis) was synthesized using in vitro transcription. The target mRNA was transfected into HEK 293T cells to evaluate protein expression levels and assess its immunogenicity. Finally, bioinformatic approaches were employed to analyze potential antigenic epitopes. Results: In this study, the successfully constructed recombinant plasmids pIVTRup-omp16 and pIVTRup-omp19 were utilized to synthesize omp16-mRNA and omp19-mRNA, each approximately 600 nt in length. Western blot analysis detected the expression of proteins with molecular weights of 16 kDa and 19 kDa in HEK 293T cells at 24 h post-transfection with mRNA. Purified rOmp16 and rOmp19 had good immunogenicity, which could specifically bind to serum antibodies of brucellosis patients. rOmp16 had stronger immunogenicity than rOmp19. Epitope prediction showed that Omp16 contained seven epitopes and Omp19 contained six epitopes. In addition, Omp16 and Omp19 could form stable complexes with target receptors. Simulated immunization with Omp16 and Omp19 proteins significantly activated both CD4⁺ and CD8⁺ T cells. Conclusions: The immunogenic proteins were successfully expressed in cells based on the mRNA fragments synthesized from omp16 and omp19 genes of B. melitensis, which was a preliminary exploration for the preparation of B. melitensis mRNA vaccine. Full article

Background: Avian pathogenic Escherichia coli (APEC) are significant bacterial pathogens that cause economic losses in the poultry industry and can pose a potential foodborne zoonotic risk. Herein, we examined APEC distribution and antimicrobial resistance in E. coli isolated from slaughtered broiler chickens in northern Thailand. Methods: PCR was used to classify APEC as either virulent or avirulent on 108 stored E. coli strains, as well as to perform Clermont phylotyping. Antimicrobial susceptibility to ciprofloxacin, cefotaxime, ceftazidime, imipenem, and colistin was examined. Results: Of the 108 E. coli strains, 101 (93.5%) isolates were APEC, and the remaining isolates were non-APEC. Among the APEC isolates, 58.4% were classified as virulent APEC; these isolates showed a statistically significant association with phylogroups F and C and (n = 54, 56.8%) more frequently exhibited a ciprofloxacin-resistant phenotype than avirulent APEC (n = 35, 36.8%). Among the ten APEC virulence genes, hlyF, iroC, iroN, iutA, O78, and ompT were significantly associated with virulent APEC. Conclusions: This study reveals a high prevalence of virulent APEC with fluoroquinolone resistance in slaughtered broiler chickens. Almost all virulent APEC strains belong to phylogroups F and C. The prediction of virulent APEC using hlyF, iroC, iroN, iutA, O78, and ompT may be useful. Full article

The TonB-dependent receptors (TBDRs) FepA and FhuA transport the siderophores ferric enterobactin (FeEnt) and ferrichrome (Fc), respectively, through the Gram-negative bacterial outer membrane. Their uptake mechanism involves conformational change in an ~150 residue N-terminal luminal domain (NTLD), located within their C-terminal β-barrel (CTβB) channels. We identified four internal sites (1–4) in TBDR that form a conserved network of ion pairs encircling the NTLD-CTβB interface. We tested the mechanistic importance of these electrostatic interactions by engineering systematic Ala substitutions in FepA and FhuA for the acidic or basic side chains that comprise them. Siderophore nutrition assays, colicin susceptibility tests and fluorescence spectroscopic uptake measurements of the mutants showed the importance of site-2, that adheres the base of NL1/Nβ3 and Nβ5 of the NTLD to β14 and β17 on the interior of the CTβB. Disruption of electrostatic bonds at site-2 reduced or eliminated ferric siderophore uptake and severely curtailed colicin susceptibility. Despite these reductions in ligand transport, fluorescent spectroscopic binding measurements showed that the site-2 mutations did not alter the affinity of FepA for FeEnt, nor FhuA for Fc. Elimination of ionic interactions at the three other locations in FepA (sites-1, -3, -4) did not reduce FeEnt uptake. Lastly, the disruption of ionic bonding at site-2 in FepA rendered it more susceptible to proteolysis, in part by OmpT, suggesting that ablation of ionic interactions in site-2 destabilized the NTLD within the CTβB. Overall, the experiments demonstrated that the ion pairs at site-2 in FepA and FhuA, that are evolutionarily conserved in the TBDR superfamily, are essential to the movement of ferric siderophores through the CTβB into the periplasm. Full article

We propose a low-complexity hybrid beamforming method for massive Multiple-Input Multiple-Output (MIMO) systems that is robust to Channel State Information (CSI) estimation errors. These errors stem from hardware impairments, pilot contamination, limited training, and fast fading, causing spectral-efficiency loss. However, existing hybrid beamforming solutions typically either assume near-perfect CSI or rely on greedy/black-box designs without an explicit mechanism to regularize the error-distorted singular modes, leaving a gap in unified, low-complexity, and theoretically grounded robustness. We unfold the Alternating Direction Method of Multipliers (ADMM) into a trainable Deep Learning (DL) network, termed DL-ADMM, to jointly optimize Radio-Frequency (RF) and baseband precoders and combiners. In DL-ADMM, the ADMM update mappings are learned (layer-wise parameters and projections) to amortize the joint RF/baseband optimization, whereas Regularized Singular Value Decomposition (RSVD) acts as an analytical regularizer that reshapes the observed channel’s singular values to suppress noise amplification under imperfect CSI. RSVD is integrated to stabilize singular modes and curb noise amplification, yielding a unified and scalable design. For ${\sigma }_e^2=0.1$, the proposed DL-ADMM-Reg achieves approximately 8–11 bits/s/Hz higher spectral efficiency than Orthogonal Matching Pursuit (OMP) at Signal-to-Noise Ratio (SNR) $=20$–40 dB, while remaining within <1 bit/s/Hz of the digital-optimal benchmark across both $(N_t,N_r)=(32,32)$ and $(64,64)$ settings. Simulations confirm higher spectral efficiency and robustness than OMP and Adaptive Phase Shifters (APSs). Full article

Burkholderia pseudomallei complex and B. cepacia complex are two evolutionary distinct clades of pathogens causing human disease. Most vaccine efforts have focused on the former group largely due to their biothreat status and global disease burden. It has been proposed that a vaccine could be developed that simultaneously protects against both groups of Burkholderia by specifically targeting conserved antigens. Only a few studies have set out to identify which antigens may be optimal targets for such a vaccine. We have previously assessed the ability of three highly conserved B. pseudomallei antigens, namely OmpA1, OmpA2, and Pal, coupled to gold nanoparticle vaccines, to protect mice against a homotypic B. pseudomallei challenge. Here, we have expanded our study by demonstrating that antibodies to each of these proteins show varying levels of reactivity to homologues in B. cepacia complex, with OmpA2 antibodies exhibiting the highest cross-reactivity. Remarkably, some nanovaccine immunized mice, particularly those that received OmpA2, produced antibodies that bind Pseudomonas aeruginosa, which harbors distantly related homologous proteins. T cells elicited to Pal and OmpA2 responded to stimulation with B. cepacia complex-derived homologues. Our study supports incorporation of these antigens, particularly OmpA2, for the development of a pan-Burkholderia vaccine. Full article

This research utilized the CRISPR/Cas9 editing method to generate six mutant strains of Escherichia coli (E. coli) DH5α targeting specific genes. The functional characterization and phenotypic analysis confirmed the regulatory roles of these genes in modifying membrane permeability. The variations in membrane permeability among the mutant strains were assessed by measuring electrical conductivity, ortho-nitrophenyl-β-D-galactopyranoside (ONPG) hydrolysis, and propidium iodide (PI) fluorescence, with E. coli DH5α:ompA′ exhibiting the most pronounced increase in membrane permeability. The function of these genes in transformation was analyzed from physicochemical and microscopic perspectives. Assays of plasmid transformation efficiency revealed a significant enhancement in the E. coli DH5α:ompA′ mutant strain, underscoring the critical function of outer membrane proteins in DNA acquisition. Permeability simulations were performed utilizing the E. coli DH5α:ompA′ mutant strain, grounded in a previously established model. The quantitative correlation between transformation efficiency and membrane permeability in this mutant conformed to the equation T = aP + c. Full article

This paper presents a comprehensive study on the feasibility and implications of a CO₂ injection simulation in the Syderiai deep saline aquifer of Lithuania, focusing on leakage, geo-mechanical aspects, and geo-chemical aspects. The Syderiai aquifer, characterized by its sandstone formation covered by shaly rocks, is considered a potential site for CO₂ geological storage in Lithuania. Using 3D mechanistic models developed in T-navigator software, we conducted extensive simulations to analyze CO₂ storage behavior and associated impacts. The leakage study examines various scenarios to assess the impact of fracture permeability, layer-wise heterogeneity, and fracture position on CO₂ injection and leakage volumes. Results indicate that while fracture permeability influences CO₂ migration dynamics, its impact on both free and dissolved CO₂ leakage volumes is minimal, highlighting that leakage behavior is more dependent on the presence of fractures than their permeability. Geo-mechanical analysis reveals the effects of CO₂ injection on the bulk modulus and shear modulus of sandstone and shale formations, highlighting changes in compaction and cementation. The geo-chemical study was performed using TOUGHREACT software V4.13-OMP to investigate the distribution of pH, porosity change, and free CO₂ over 1000-years following 10-year CO₂ injection. Results demonstrate the acidifying effect of CO₂ injection and its implications for the caprock–reservoir interface over time. The findings offer valuable perspectives on the feasibility and consequences of CO₂ geological storage in the Syderiai deep saline aquifer, highlighting the importance of incorporating leakage, geo-mechanical aspects, and geo-chemical aspects for implementing efficient CO₂ storage. Full article

This study presents a comprehensive validation of total ozone columns from ozone profile (O₃P) and total ozone column (O₃T) products measured by the Geostationary Environment Monitoring Spectrometer (GEMS), through comparisons with Pandora, Ozone Mapping and Profiler Suite (OMPS) and TROPOspheric Monitoring Instrument (TROPOMI). O₃P version 3.0 demonstrates reduced dependence on viewing geometry compared to version 2.0, whereas the O₃T product shows a consistent offset between versions (v2.0 vs. v2.1). In comparison with Pandora, O₃P exhibits seasonal bias patterns similar to those seen in TROPOMI and OMPS, ranging from −2% in summer to +5% in winter. However, O₃T maintains abnormally persistent negative biases across seasons and times of day, along with a long-term degradation of 2–3% from 2021 to 2024. These findings suggest that O₃T biases likely result from uncorrected radiometric biases rather than algorithmic limitations. Validation metrics further highlight inconsistencies in O₃T, including a lower regression slope (~0.95) in the mid-latitude and higher root mean square errors in the low-latitude (~5%), compared to the other products (near 1.0 and 1–3%, respectively). Overall, O₃P outperforms TROPOMI and OMPS across most validation metrics in mid-latitudes and performs similarly at low latitudes. Full article