Search Results (28)

Background/Objectives: Software is now core infrastructure in biomedical science, yet fragmented workflows across subfields hinder reproducibility and delay the translation of data into actionable decisions. There is a critical need for a cross-disciplinary synthesis to bridge these silos and establish a unified framework for software maturity. This narrative review addresses this gap by synthesizing representative software ecosystems across three major pillars: bioinformatics, molecular modeling/simulations, and epidemiology/public health. Methods: A narrative review of articles indexed in PubMed/NCBI, Web of Science, and Scopus between 2000 and 2025 was conducted. Domain-specific terms related to bioinformatics, molecular modeling, docking, molecular dynamics, epidemiology, public health, and workflow management were combined with software- and algorithm-focused keywords. Studies describing, validating, or applying documented tools with biomedical relevance were included. Results: Across domains, mature data standards and reference resources (e.g., FASTQ, BAM/CRAM, VCF, mzML), widely adopted platforms (e.g., BLAST+ (v2.16.0, NCBI, Bethesda, MD, USA), Bioconductor (v3.20, Bioconductor Foundation, Seattle, WA, USA), AutoDock Vina (v1.2.5, Scripps Research, La Jolla, CA, USA), GROMACS (v2024.3, GROMACS Team, Stockholm, Sweden), Epi Info (v7.2.6, CDC, Atlanta, GA, USA), QGIS (v3.40, QGIS.org, Gossau, Switzerland), and increasing use of workflow engines were identified. Software pipelines routinely transform molecular and surveillance data into interpretable features supporting hypothesis generation. Conclusions: Integrated, standards-based, and validated software pipelines can shorten the path from measurement to decision in biomedicine and public health. Future progress depends on reproducibility practices, benchmarking, user-centered design, portable implementations, and responsible deployment of machine learning. Full article

Ensuring the structural integrity of road infrastructure is vital for transportation safety and long-term sustainability. This study presents a lightweight and accurate pavement crack detection framework named SpcNet, which integrates a Sparse Encoding Module, ConvNeXt V2-based decoder, and a Binary Attention Module (BAM) within an asymmetric encoder–decoder architecture. The proposed method first applies a random masking strategy to generate sparse pixel inputs and employs sparse convolution to enhance computational efficiency. A ConvNeXt V2 decoder with Global Response Normalization (GRN) and GELU activation further stabilizes feature extraction, while the BAM, in conjunction with Channel and Spatial Attention Bridge (CAB/SAB) modules, strengthens global dependency modeling and multi-scale feature fusion. Comprehensive experiments on four public datasets demonstrate that SpcNet achieves state-of-the-art performance with significantly fewer parameters and lower computational cost. On the Crack500 dataset, the method achieves a precision of 91.0%, recall of 85.1%, F1 score of 88.0%, and mIoU of 79.8%, surpassing existing deep-learning-based approaches. These results confirm that SpcNet effectively balances detection accuracy and efficiency, making it well-suited for real-world pavement condition monitoring. Full article

Background: Monoclonal antibodies play an important role in therapeutic and analytical applications. For recombinant expression, the coding sequences of the variable regions of the heavy and light chains are required. In addition, cloning antibody sequences, including constant regions, reduces the impact of hybridoma cell loss and ensures preservation of the naturally occurring full antibody sequence. Method: We combined amplification of IgG antibody variable regions from hybridoma mRNA with an advanced method for full-length cloning of monoclonal antibodies in a simple two-step workflow. Following Sanger sequencing and evaluation of consensus sequences, the best matching variable, diversity, and joining (V-(D-)J) gene segments were identified according to identity scores from IgBLAST reference sequences. Simultaneously, the mouse IgG subclass was determined at the DNA level based on isotype-specific sequence patterns in the C_H1 domain. Knowing the DNA sequence of V-(D-)J recombination responsible for the complementary determining region 3 (CDR 3), variable region-specific primers were designed and used to amplify the corresponding antibody constant regions. Results: To verify the approach, we applied it to the hybridoma clone BAM-CCMV-29-81 and obtained identical full-length antibody sequences as with RNA Illumina sequencing. Further validation at the protein level using an established MALDI-TOF MS-fingerprinting protocol showed that five out of six genetically encoded CDR domains of the monoclonal antibody BAM-CCMV-29-81 could be efficiently correlated. Conclusion: This simple, streamlined method enables the cost-effective determination of the full-length sequence of monoclonal antibodies from hybridoma cell lines, with the added benefit of obtaining the DNA sequence of the antibody ready for recombinant expression. Full article

This report is on Co and Ti substituted M-type barium and strontium hexagonal ferrites that are reported to be single phase multiferroics due to a transition from Neel type ferrimagnetic order to a spiral spin structure that is accompanied by a ferroelectric polarization in an applied magnetic field. The focus here is the nature of magnetoelectric (ME) interactions in the bilayers of ferroelectric PZT and Co and Ti substituted BaM and SrM. The ME coupling in the ferrite-PZT bilayers arise due to the transfer of magnetostriction-induced mechanical deformation in a magnetic field in the ferrite resulting in an induced electric field in PZT. Polycrystalline Co and Ti doped ferrites, Ba (CoTi)_x Fe_12−2xO_19, (BCTx), and Sr (CoTi)_x Fe_12−2xO₁₉ (SCTx) (x = 0–4) were found to be free of impurity phases for all x-values except for SCTx, which had a small amount of α-Fe₂O₃ in the X-ray diffraction patterns for x ≤ 2.0. The magnetostriction for the ferrites increased with applied filed H to a maximum value of around 2 to 6 ppm for H~5 kOe. BCTx/SCTx samples showed ferromagnetic resonance (FMR) for x = 1.5–2.0, and the estimated anisotropy field was on the order of 5 kOe. The magnetization increased with the amount of Co and Ti doping, and it decreased rapidly with x for x > 1.0. Measurements of ME coupling strengths were conducted on the bilayers of BCTx/SCTx platelets bonded to PZT. The bilayer was subjected to an AC and DC magnetic field H, and the magnetoelectric voltage coefficient (MEVC) was measured as a function of H and frequency of the AC field. For BCTx-PZT, the maximum value of MEVC at low frequency was ~5 mV/cm Oe, and a 40-fold increase at electromechanical resonance (EMR). SCTx–PZT composites also showed a similar behavior with the highest MEVC value of ~14 mV/cm Oe at low frequencies and ~200 mV/cm Oe at EMR. All the bilayers showed ME coupling for zero magnetic bias due to the magnetocrystalline anisotropy field in the ferrite that provided a built-in bias field. Full article

Space-time image velocimetry (STIV) plays an important role in river velocity measurement due to its safety and efficiency. However, its practical application is affected by complex scene conditions, resulting in significant errors in the accurate estimation of texture angles. This paper proposes a method to predict the texture angles in frequency domain images based on an improved ShuffleNetV2. The second 1 × 1 convolution in the main branch of the downsampling unit and basic unit is deleted, the kernel size of the depthwise separable convolution is adjusted, and a Bottleneck Attention Module (BAM) is introduced to enhance the ability of capturing important feature information, effectively improving the precision of texture angles. In addition, the measured data from a current meter are used as the standard for comparison with established and novel approaches, and this study further validates its methodology through comparative experiments conducted in both artificial and natural river channels. The experimental results at the Agu, Panxi, and Mengxing hydrological stations demonstrate that the relative errors of the discharge measured by the proposed method are 2.20%, 3.40%, and 2.37%, and the relative errors of the mean velocity are 1.47%, 3.64%, and 1.87%, which affirms it has higher measurement accuracy and stability compared with other methods. Full article

To lighten the workload of train drivers and enhance railway transportation safety, a novel and intelligent method for railway turnout identification is investigated based on semantic segmentation. More specifically, a railway turnout scene perception (RTSP) dataset is constructed and annotated manually in this paper, wherein the innovative concept of side rails is introduced as part of the labeling process. After that, based on the work of Deeplabv3+, combined with a lightweight design and an attention mechanism, a railway turnout identification network (RTINet) is proposed. Firstly, in consideration of the need for rapid response in the deployment of the identification model on high-speed trains, this paper selects the MobileNetV2 network, renowned for its suitability for lightweight deployment, as the backbone of the RTINet model. Secondly, to reduce the computational load of the model while ensuring accuracy, depth-separable convolutions are employed to replace the standard convolutions within the network architecture. Thirdly, the bottleneck attention module (BAM) is integrated into the model to enhance position and feature information perception, bolster the robustness and quality of the segmentation masks generated, and ensure that the outcomes are characterized by precision and reliability. Finally, to address the issue of foreground and background imbalance in turnout recognition, the Dice loss function is incorporated into the network training procedure. Both the quantitative and qualitative experimental results demonstrate that the proposed method is feasible for railway turnout identification, and it outperformed the compared baseline models. In particular, the RTINet was able to achieve a remarkable mIoU of 85.94%, coupled with an inference speed of 78 fps on the customized dataset. Furthermore, the effectiveness of each optimized component of the proposed RTINet is verified by an additional ablation study. Full article

Vibrio parahaemolyticus is an important foodborne bacterium that causes severe gastroenteritis following the consumption of contaminated seafood. To identify V. parahaemolyticus and determine its pathogenicity, the U.S. Food and Drug Administration (FDA)’s Bacteriological Analytical Manual (BAM) recommends a multiplex polymerase chain reaction (PCR) protocol to simultaneously detect the species-specific thermolabile hemolysin (tlh) gene and the pathogenic thermostable-related hemolysin (trh) and thermostable-direct hemolysin (tdh) genes. However, this assay has shown two limitations: difficulty in separating the amplicons of the trh (486 bp) and tlh (450 bp) genes due to their highly similar sizes, and the weaker band exhibited by the tdh gene amplicon (270 bp). The present study aimed to improve the BAM’s multiplex PCR assay by separating the three amplicons with similar intensity. A new primer set was applied for the tlh gene (369 bp) alongside the existing primers for the trh and tdh genes. The amplicons for the three genes were effectively separated by electrophoresis on a 2% tris-borate-EDTA (TBE) agarose gel within 45 min. Primer concentrations of 0.25 µM for three genes produced a significant amount of amplicons among various combinations of primer concentrations with 35 PCR cycles. This assay exhibited a detection limit of 10 pg of bacterial DNA, demonstrating its high sensitivity. It did not display amplicons from nine Vibrio species known to be human pathogens or from 18 well-documented foodborne pathogens. Therefore, the present multiplex PCR protocol could help overcome the limitations of existing assays and provide a more reliable method for detecting the three genes of V. parahaemolyticus. Full article

Accurate identification of Seriola dumerili (SD) offers crucial technical support for aquaculture practices and behavioral research of this species. However, the task of discerning S. dumerili from complex underwater settings, fluctuating light conditions, and schools of fish presents a challenge. This paper proposes an intelligent recognition model based on the YOLOv8 network called SD-YOLOv8. By adding a small object detection layer and head, our model has a positive impact on the recognition capabilities for both close and distant instances of S. dumerili, significantly improving them. We construct a convenient S. dumerili dataset and introduce the deformable convolution network v2 (DCNv2) to enhance the information extraction process. Additionally, we employ the bottleneck attention module (BAM) and redesign the spatial pyramid pooling fusion (SPPF) for multidimensional feature extraction and fusion. The Inner-MPDIoU bounding box regression function adjusts the scale factor and evaluates geometric ratios to improve box positioning accuracy. The experimental results show that our SD-YOLOv8 model achieves higher accuracy and average precision, increasing from 89.2% to 93.2% and from 92.2% to 95.7%, respectively. Overall, our model enhances detection accuracy, providing a reliable foundation for the accurate detection of fishes. Full article

This study compared the efficiency of advanced supercritical CO₂ extraction (SC-CO₂) and conventional Soxhlet extraction (SE) in the isolation of lipophilic bioactive molecules (BAMs) from the oils of different sea buckthorn (SB) berries (Leikora and Ascola). A SB cake, a valuable by-product of oil extraction, was analyzed for phenolic compounds and antioxidant activity (AA). For this purpose, ultrasound-assisted extraction (UAE) with 70% (v/v) ethanol was optimized, and the following optimal UAE conditions were determined: ultrasonic power of 60%, temperature of 50 °C, and extraction time of 20 min. The individual BAMs in the oils and cake extracts were analyzed chromatographically, while the AAs were determined using the ORAC method. The oils extracted with SC-CO₂ had a higher content of lipophilic BAMs and a higher AA value than the oils extracted with SE. Palmitic and palmitoleic acids, β-sitosterol, and α-tocopherol dominated the Leikora oil, while a higher content of oleic, linoleic, and α-linolenic acids and carotenoids was found in the Ascola oil. The highest phenolic content was found in the Ascola cake, with the flavonols isorhamnetin-3-hexoside, isorhamnetin-3-rutinoside, and quercetin-3-glucoside being the most abundant. Oil and cake extracts of the Ascola variety also had a higher AA. Full article

The magnetoelectric effect (ME) is an important strain mediated-phenomenon in a ferromagnetic-piezoelectric composite for a variety of sensors and signal processing devices. A bias magnetic field, in general, is essential to realize a strong ME coupling in most composites. Magnetic phases with (i) high magnetostriction for strong piezomagnetic coupling and (ii) large anisotropy field that acts as a built-in bias field are preferred so that miniature, ME composite-based devices can operate without the need for an external magnetic field. We are able to realize such a magnetic phase with a composite of (i) barium hexaferrite (BaM) with high magnetocrystalline anisotropy field and (ii) nickel ferrite (NFO) with high magnetostriction. The BNx composites, with (100 − x) wt.% of BaM and x wt.% NFO, for x = 0–100, were prepared. X-ray diffraction analysis shows that the composites did not contain any impurity phases. Scanning electron microscopy images revealed that, with an increase in NFO content, hexagonal BaM grains become prominent, leading to a large anisotropy field. The room temperature saturation magnetization showed a general increase with increasing BaM content in the composites. NFO rich composites with x ≥ 60 were found to have a large magnetostriction value of around −23 ppm, comparable to pure NFO. The anisotropy field H_A of the composites, determined from magnetization and ferromagnetic resonance (FMR) measurements, increased with increasing NFO content and reached a maximum of 7.77 kOe for x = 75. The BNx composite was cut into rectangular platelets and bonded with PZT to form the bilayers. ME voltage coefficient (MEVC) measurements at low frequencies and at mechanical resonance showed strong coupling at zero bias for samples with x ≥ 33. This large in-plane H_A acted as a built-in field for strong ME effects under zero external bias in the bilayers. The highest zero-bias MEVC of ~22 mV/cm Oe was obtained for BN75-PZT bilayers wherein BN75 also has the highest H_A. The Bilayer of BN95-PZT showed a maximum MEVC ~992 mV/cm Oe at electromechanical resonance at 59 kHz. The use of hexaferrite–spinel ferrite composite to achieve strong zero-bias ME coupling in bilayers with PZT is significant for applications related to energy harvesting, sensors, and high frequency devices. Full article

Blueberry anthocyanins are water-soluble natural pigments that can be used as both natural antioxidants and natural colorants. However, their structural instability greatly limits their application in the food, pharmaceutical, and cosmetic industries. In this study, blueberry anthocyanin microcapsules (BAM) and blueberry anthocyanin liposomes (BAL) were fabricated based on blueberry anthocyanins. Film dispersion methods were used to prepare the BAL. Their preparation processes were optimized and compared to improve the stability of the blueberry anthocyanins following exposure to light and high temperatures. The BAM were prepared through complex phase emulsification. The blueberry anthocyanins were protected by the shell materials composed of sodium alginate after being formed into BAM. Under the optimal conditions, the embedding rate of BAM and BAL can reach as high as 96.14% and 81.26%, respectively. In addition, the particle size, zeta potential, microtopography, and structure feature information of the BAM and BAL were compared. The average particle sizes of the BAM and BAL were 9.78 μm and 290.2 nm, respectively, measured using a laser particle size analyzer, and the zeta potentials of the BAM and BAL were 34.46 mV and 43.0 mV, respectively. In addition, the optimal preparation processes were determined through single-factor and response surface optimization experiments. The most important factors in the single-factor experiment for the preparation of microcapsules and liposomes were the content of CaCl₂ and the amount of anthocyanin. The preservation rates in the light and dark were also compared, and the thermal stabilities of the BAM and BAL were characterized through differential thermal scanning. The results showed that both the BAM and BAL maintained the stability of blueberry anthocyanins, and no significant difference was found between the indices used to evaluate their stability. The results of this study provide theoretical support for the development of effective systems to maintain the stability of anthocyanins, thereby improving their bioavailability after ingestion by humans. Full article

We report a new industrial application of aluminum magnesium boride AlMgB₁₄ (BAM) coatings to enhance the hardness of tungsten carbide ceramic (WC-Co) and high-speed steel tools. BAM films were deposited by RF magnetron sputtering of a single dense stoichiometric ceramic target onto commercial WC-Co turning inserts and R6M5 steel drill bits. High target sputtering power and sufficiently short target-to-substrate distance were found to be critical processing conditions. Very smooth (6.6 nm RMS surface roughness onto Si wafers) and hard AlMgB₁₄ coatings enhance the hardness of WC-Co inserts and high-speed R6M5 steel by a factor of two and three, respectively. Complete coating spallation failure occurred at a scratch adhesion strength of 18 N. High work of adhesion and low friction coefficient, estimated for BAM onto drill bits, was as high as 64 J/m² and as low as 0.07, respectively, more than twice the surpass characteristics of N-doped diamond-like carbon (DLC) films deposited onto nitride high-speed W6Mo5Cr4V2 steel. Full article

Two poly(3,4-ethylenedioxythiophene) polyrotaxanes (PEDOT∙TMe-βCD and PEDOT∙TMe-γCD) end-capped by pyrene (Py) were synthesized by oxidative polymerization of EDOT encapsulated into TMe-βCD or TMe-γCD cavities with iron (III) chloride (FeCl₃) in water and chemically characterized. The effect of TMe-βCD or TMe-γCD encapsulation of PEDOT backbones on the molecular weight, thermal stability, and solubility were investigated in depth. UV–vis absorption, fluorescence (F_L), phosphorescence (P_H), quantum efficiencies, and lifetimes in water and acetonitrile were also explored, together with their surface morphology and electrical properties. Furthermore, dynamic light scattering was used to study the hydrodynamic diameter (DH) and z-potential (ZP-ζ) of the water soluble fractions of PEDOT∙TMe-βCD and PEDOT∙TMe-γCD. PEDOT∙TMe-βCD and PEDOT∙TMe-γCD exhibited a sharp monodisperse peak with a DH of 55 ± 15 nm and 122 ± 32 nm, respectively. The ZP-ζ value decreased from −31.23 mV for PEDOT∙TMe-βCD to −20.38 mV for PEDOT∙TMe-γCD, indicating that a negatively charged layer covers their surfaces. Surface pressure–area isotherms and Brewster angle microscopy (BAM) studies revealed the capability of the investigated compounds to organize into sizeable and homogeneous 2D supramolecular assemblies at the air–water interface. The control of the 2D monolayer organization through the thermodynamic parameters of PEDOT∙TMe-βCD and PEDOT∙TMe-γCD suggests potential for a wide range of optoelectronic applications. Full article

Transmembrane proteins span lipid bilayer membranes and serve essential functions in all living cells. Membrane-inserted domains are of either α-helical or β-barrel structure. Despite their biological importance, the biophysical mechanisms of the folding and insertion of proteins into membranes are not well understood. While the relative composition of the secondary structure has been examined by circular dichroism spectroscopy in folding studies for several outer membrane proteins, it is currently not known how individual β-strands fold. Here, the folding and insertion of the β-barrel assembly machinery protein A (BamA) from the outer membrane of Escherichia coli into lipid bilayers were investigated, and the formation of strand nine (β₉) of BamA was examined. Eight single-cysteine mutants of BamA were overexpressed and isolated in unfolded form in 8 M urea. In each of these mutants, one of the residues of strand β₉, from R572 to V579, was replaced by a cysteine and labeled with the fluorophore IAEDANS for site-directed fluorescence spectroscopy. Upon urea-dilution, the mutants folded into the native structure and were inserted into lipid bilayers of dilauroylphosphatidylcholine, similar to wild-type BamA. An aqueous and a membrane-adsorbed folding intermediate of BamA could be identified by strong shifts in the intensity maxima of the IAEDANS fluorescence of the labeled mutants of BamA towards shorter wavelengths, even in the absence of lipid bilayers. The shifts were greatest for membrane-adsorbed mutants and smaller for the inserted, folded mutants or the aqueous intermediates. The spectra of the mutants V573C-, L575C-, G577C-, and V579C-BamA, facing the lipid bilayer, displayed stronger shifts than the spectra recorded for the mutants R572C-, N574C-, T576C-, and K578C-BamA, facing the β-barrel lumen, in both the membrane-adsorbed form and the folded, inserted form. This alternating pattern was neither observed for the IAEDANS spectra of the unfolded forms nor for the water-collapsed forms, indicating that strand β₉ forms in a membrane-adsorbed folding intermediate of BamA. The combination of cysteine scanning mutagenesis and site-directed fluorescence labeling is shown to be a valuable tool in examining the local secondary structure formation of transmembrane proteins. Full article

In this study, we evaluated the performance of the Brazilian Global Atmospheric Model (BAM), in its version 2.2.1, in the representation of the surface variables solar radiation, temperature (maximum, minimum, and average), and wind speed. Three experiments were carried out for the period from 2016 to 2022 under three different aerosol conditions (constant (CTE), climatological (CLIM), and equal to zero (ZERO)), discarding the first year as a spin-up period. The observations came from a high-resolution gridded analysis that provides Brazil with robust data based on observations from surface stations on a daily scale from 1961 to 2020; therefore, combining the BAM outputs with the observations, our intercomparison period took place from 2017 to 2020, for three timescales: daily, 10-day average, and monthly, targeting different applications. In its different simulations, BAM overestimated solar radiation throughout Brazil, especially in the Amazon; underestimated temperature in most of the northeast, southeast, and south regions; and overestimated in parts of the north and mid-west; while wind speed was only not overestimated in the Amazon region. In relative terms, the simulations with constant aerosol showed better performance than the others, followed by climatological conditions and zero aerosol. The dexterity indices applied in the intercomparison between BAM and observations indicate that BAM needs adjustments and calibration to better represent these surface variables. Where model deficiencies have been identified, these can be used to drive model development and further improve the predictive capabilities. Full article