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PloS One 2024Many newborn screening programs worldwide have introduced screening for diseases using DNA extracted from dried blood spots (DBS). In Germany, DNA-based assays are...
BACKGROUND
Many newborn screening programs worldwide have introduced screening for diseases using DNA extracted from dried blood spots (DBS). In Germany, DNA-based assays are currently used to screen for severe combined immunodeficiency (SCID), spinal muscular atrophy (SMA), and sickle cell disease (SCD).
METHODS
This study analysed the impact of pre-analytic DNA carry-over in sample preparation on the outcome of DNA-based newborn screening for SCID and SMA and compared the efficacy of rapid extraction versus automated protocols. Additionally, the distribution of T cell receptor excision circles (TREC) on DBS cards, commonly used for routine newborn screening, was determined.
RESULTS
Contaminations from the punching procedure were detected in the SCID and SMA assays in all experimental setups tested. However, a careful evaluation of a cut-off allowed for a clear separation of true positive polymerase chain reaction (PCR) amplifications. Our rapid in-house extraction protocol produced similar amounts compared to automated commercial systems. Therefore, it can be used for reliable DNA-based screening. Additionally, the amount of extracted DNA significantly differs depending on the location of punching within a DBS.
CONCLUSIONS
Newborn screening for SMA and SCID can be performed reliably. It is crucial to ensure that affected newborns are not overlooked. Therefore a carefully consideration of potential contaminating factors and the definition of appropriate cut-offs to minimise the risk of false results are of special concern. It is also important to note that the location of punching plays a pivotal role, and therefore an exact quantification of TREC numbers per μl may not be reliable and should therefore be avoided.
Topics: Humans; Neonatal Screening; Infant, Newborn; Muscular Atrophy, Spinal; Severe Combined Immunodeficiency; DNA; Dried Blood Spot Testing; High-Throughput Screening Assays; Polymerase Chain Reaction
PubMed: 38941330
DOI: 10.1371/journal.pone.0306329 -
Materials (Basel, Switzerland) Jun 2024Rapid industrial growth is associated with an increase in the production of environmentally harmful waste. A potential solution to significantly reduce pollution is to...
Rapid industrial growth is associated with an increase in the production of environmentally harmful waste. A potential solution to significantly reduce pollution is to replace current synthetic materials with readily biodegradable plastics. Moreover, to meet the demands of technological advancements, it is essential to develop materials with unprecedented properties to enhance their functionality. Polysaccharide composites demonstrate significant potential in this regard. Polysaccharides possess exceptional film-forming abilities and are safe for human use, biodegradable, widely available, and easily modifiable. Unfortunately, polysaccharide-based films fall short of meeting all expectations. To address this issue, the current study focused on incorporating carbon quantum dots (CQDs), which are approximately 10 nm in size, into the structure of a starch/chitosan biocomposite at varying concentrations. This modification has improved the mechanical properties of the resulting nanocomposites. The inclusion of nanoparticles led to a slight reduction in solubility and an increase in the swelling degree. The optical characteristics of the obtained films were influenced by the presence of CQDs, and the fluorescence intensity of the nanocomposites changed due to the specific heavy metal ions and amino acids used. Consequently, these nanocomposites show great potential for detecting these compounds. Cellular viability assessments and comet assays confirm that the resulting nanocomposites do not exhibit any cytotoxic properties based on this specific analytic method. The tested nanocomposites with the addition of carbon quantum dots (NC/CD II and NC/CD III) were characterised by greater genotoxicity compared to the negative control. The positive control, the starch/chitosan composite alone, was also characterised by a greater induction of chromatin damage in mouse cells compared to a pure mouse blood sample.
PubMed: 38930336
DOI: 10.3390/ma17122967 -
Biomedicines Jun 2024According to the World Health Organization, ischemic stroke is the second leading cause of death in the world. Frequently, it is caused by brachiocephalic artery (BCA)...
According to the World Health Organization, ischemic stroke is the second leading cause of death in the world. Frequently, it is caused by brachiocephalic artery (BCA) atherosclerosis. Timely detection of atherosclerosis and its unstable course can allow for a timely response to potentially dangerous changes and reduce the risk of vascular complications. Omics technologies allow us to identify new biomarkers that we can use in diagnosing diseases. This research included 90 blood plasma samples. The study group comprised 52 patients with severe atherosclerotic lesions BCA, and the control group comprised 38 patients with no BCA atherosclerosis. Targeted and panoramic lipidomic profiling of their blood plasma was carried out. There was a statistically significant difference ( < 0.05) in the values of the indices saturated fatty acids (FAs), unsaturated FAs, monounsaturated FAs, omega-3, and omega-6. Based on the results on the blood plasma lipidome, we formed models that have a fairly good ability to determine atherosclerotic lesions of the brachiocephalic arteries, as well as a model for identifying unstable atherosclerotic plaques. According only to the panoramic lipidome data, divided into groups according to stable and unstable atherosclerotic plaques, a significant difference was taken into account: value < 0.05 and abs (fold change) > 2. Unfortunately, we did not observe significant differences according to the established plasma panoramic lipidome criteria between patients with stable and unstable plaques. Omics technologies allow us to obtain data about any changes in the body. According to our data, statistically significant differences in lipidomic profiling were obtained when comparing groups with or without BCA atherosclerosis.
PubMed: 38927486
DOI: 10.3390/biomedicines12061279 -
Journal of Chemical Theory and... Jun 2024Recently Lu and Gao [ , (33), 7762-7769] published a new, rigorous density functional theory for excited states and proved that the projection of the kinetic and...
Recently Lu and Gao [ , (33), 7762-7769] published a new, rigorous density functional theory for excited states and proved that the projection of the kinetic and electron-repulsion operators into the subspace of the lowest electronic states are a universal functional of the matrix density (). This is the first attempt to find an approximation to the multistate universal functional . It is shown that (i) does not explicitly depend on the number of electronic states and (ii) is an analytic matrix functional. The Thomas-Fermi-Dirac-von Weizsäcker model and the correlation energy of the homogeneous electron gas are turned into matrix functionals guided by two principles: that each matrix functional should transform properly under basis set transformations and that the ground state functional should be recovered for a single electronic state. Lieb-Oxford-like bounds on the average kinetic and electron-repulsion energies in the subspace are given. When evaluated on the numerically exact matrix density of LiF, this simple approximation reproduces the matrix elements of the electron-repulsion operator in the basis of the exact eigenstates accurately for all bond lengths. In particular the off-diagonal elements of the effective Hamiltonian that come from the interactions of different electronic states can be calculated with the same or better accuracy than the diagonal elements. Unsurprisingly, the largest error comes from the kinetic energy functional. More exact conditions that constrain the functional form of are needed to go beyond the local density approximation.
PubMed: 38905701
DOI: 10.1021/acs.jctc.4c00330 -
Molecules (Basel, Switzerland) Jun 2024L. possesses abundant germplasm resources and holds significant value in terms of ornamental, edible, and medicinal aspects. However, the quality characteristics vary...
L. possesses abundant germplasm resources and holds significant value in terms of ornamental, edible, and medicinal aspects. However, the quality characteristics vary significantly depending on different varieties. Selection of a high-quality variety with a characteristic aroma can increase the economic value of flowers. The analytic hierarchy process (AHP) is an effective decision-making method for comparing and evaluating multiple characteristic dimensions. By applying AHP, the aromatic character of 60 varieties of flowers were analyzed and evaluated in the present study. Headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) was employed to identify volatile components in flowers. Thirteen volatile components were found to contribute to the aroma of flowers, which helps in assessing their potential applications in essential oil, aromatherapy, and medical treatment. These components include 2-phenylethanol, geraniol, linalool, nonanal, decanal, (E)--ocimene, α-farnesene, indole, nerolidol, 3-furanmethanol, 3-carene, benzaldehyde and benzenemethanol. The varieties with better aromatic potential can be selected from a large amount of data using an AHP model. This study provides a comprehensive understanding of the characteristics of the aroma components in flowers, offers guidance for breeding, and enhances the economic value of flowers.
Topics: Gas Chromatography-Mass Spectrometry; Volatile Organic Compounds; Solid Phase Microextraction; Flowers; Odorants; Acyclic Monoterpenes; Oils, Volatile; Sesquiterpenes; Phenylethyl Alcohol; Alkenes; Indoles
PubMed: 38893586
DOI: 10.3390/molecules29112712 -
The Science of the Total Environment Sep 2024Integrated health risk assessment strategies for emerging organic pollutants and heavy metals that coexist in water/soil media are lacking. Contents of perfluoroalkyl...
Integrated health risk assessment strategies for emerging organic pollutants and heavy metals that coexist in water/soil media are lacking. Contents of perfluoroalkyl compounds and potentially toxic elements in multiple media were determined by investigating a county where a landfill and a tungsten mine coexist. The spatial characteristics and sources of contaminants were predicted by Geostatistics-based and multivariate statistical analysis, and their comprehensive health risks were assessed. The average contents of perfluorooctane acid, perfluorooctanesulfonic acid, arsenic, and cadmium in groundwater were 3.21, 0.77, 1.69, and 0.14 μg L, respectively; the maximum content of cadmium in soils and rice highly reached 2.12 and 1.52 mg kg, respectively. In soils, the contribution of mine lag to cadmium was 99 %, and fertilizer and pesticide to arsenic was 59.4 %. While in groundwater, arsenic, cadmium and perfluoroalkyl compounds near the landfill mainly came from leachate leakage. Significant correlations were found between arsenic in groundwater and arsenic and cadmium in soils, as well as perfluoroalkyl compounds in groundwater and pH and sulfate. Based on these correlations, the geographically optimal similarity model predicted high-level arsenic in groundwater near the tungsten mine and cadmium/perfluoroalkyl compounds around the landfill. The combination of analytic network process, entropy weighting method and game theory-based trade-off method with risk assessment model can assess the comprehensive risks of multiple pollutants. Using this approach, a high health-risk zone located around the landfill, which was mainly attributed to the presence of arsenic, cadmium and perfluorooctanesulfonic acid, was found. Overall, perfluoroalkyl compounds in groundwater altered the spatial pattern of health risks in an arsenic‑cadmium contaminated area.
Topics: Groundwater; Water Pollutants, Chemical; Fluorocarbons; Arsenic; Environmental Monitoring; Cadmium; Risk Assessment; Soil Pollutants; Alkanesulfonic Acids; Mining; China
PubMed: 38876341
DOI: 10.1016/j.scitotenv.2024.173983 -
The Journal of Physical Chemistry... Jun 2024Quartic force fields (QFFs) define sparse potential energy surfaces (compared to semiglobal surfaces) that are the cheapest and easiest means of computing anharmonic... (Review)
Review
Quartic force fields (QFFs) define sparse potential energy surfaces (compared to semiglobal surfaces) that are the cheapest and easiest means of computing anharmonic vibrational frequencies, especially when utilized with second-order vibrational perturbation theory (VPT2). However, flat and shallow potential surfaces are exceedingly difficult for QFFs to treat through a combination of numerical noise in the often numerically computed derivatives and in competing energy factors in the composite energies often utilized to provide high-level spectroscopic predictions. While some of these issues can be alleviated with analytic derivatives, hybrid QFFs, and intelligent choices in coordinate systems, the best practice is for predicting good molecular vibrations via QFFs is to understand what they cannot do, and this manuscript documents such cases where QFFs may fail.
PubMed: 38875074
DOI: 10.1021/acs.jpclett.4c01089 -
ISME Communications Jan 2024The performance of sequence variant resolution analytic tools for metabarcoding has not yet been adequately benchmarked for high-diversity environmental samples. We...
The performance of sequence variant resolution analytic tools for metabarcoding has not yet been adequately benchmarked for high-diversity environmental samples. We therefore evaluated the sequence variant tools DADA2, Deblur, Swarm, and UNOISE, using high-diversity seafloor samples, resulting in comparisons of 1800 sequence variant tables. The evaluation was based on 30 sediment grab samples, for which 3 replica samples were collected. Each replica sample was extracted using 5 common DNA extraction kits, resulting in 450 DNA extracts which were 16S rRNA gene sequenced (V3-V4), using Illumina. Assessments included variation across replica samples, extraction kits, and denoising methods, in addition to applying prior knowledge about alpha diversity correlations toward the cosmopolitan marine archaeon with high diversity and the sulfide oxidizing with low diversity DADA2 displayed the highest variance between replicates (Manhattan distance 1.14), while Swarm showed the lowest variance (Manhattan distance 0.93). For the analysis based on prior biological knowledge, UNOISE displayed the highest alpha diversity (Simpson's D) correlation toward (Spearman rho = 0.85), while DADA2 showed the lowest (Spearman rho = 0.10). Deblur completely eliminated from the dataset. For , on the other hand, all the methods showed comparable results. In conclusion, our evaluations show that Swarm and UNOISE performed better than DADA2 and Deblur for high-diversity seafloor samples.
PubMed: 38873028
DOI: 10.1093/ismeco/ycae071 -
Frontiers in Bioengineering and... 2024Pharmaceutical manufacturing is reliant upon bioprocessing approaches to generate the range of therapeutic products that are available today. The high cost of...
Pharmaceutical manufacturing is reliant upon bioprocessing approaches to generate the range of therapeutic products that are available today. The high cost of production, susceptibility to process failure, and requirement to achieve consistent, high-quality product means that process monitoring is paramount during manufacturing. Process analytic technologies (PAT) are key to ensuring high quality product is produced at all stages of development. Spectroscopy-based technologies are well suited as PAT approaches as they are non-destructive and require minimum sample preparation. This study explored the use of a novel attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy platform, which utilises disposable internal reflection elements (IREs), as a method of upstream bioprocess monitoring. The platform was used to characterise organism health and to quantify cellular metabolites in growth media using quantification models to predict glucose and lactic acid levels both singularly and combined. Separation of the healthy and nutrient deficient cells within PC space was clearly apparent, indicating this technique could be used to characterise these classes. For the metabolite quantification, the binary models yielded values of 0.969 for glucose, 0.976 for lactic acid. When quantifying the metabolites in tandem using a multi-output partial least squares model, the corresponding value was 0.980. This initial study highlights the suitability of the platform for bioprocess monitoring and paves the way for future in-line developments.
PubMed: 38863496
DOI: 10.3389/fbioe.2024.1349473 -
Heliyon Jun 2024An analytic design of a prototype filter for M-channel maximally decimated cosine-modulated Near Perfect Reconstruction (NPR) filter banks is proposed in this work. The...
An analytic design of a prototype filter for M-channel maximally decimated cosine-modulated Near Perfect Reconstruction (NPR) filter banks is proposed in this work. The prototype filter is created using the least-square (CLS) method with weighted constraints, which is one-dimensional and requires single-parameter optimization. Compared to existing approaches, this suggested method achieves rapid convergence by analytically determining the optimal step size, ensuring the 3 dB cutoff frequency at π/2 M. The simulation results for design examples outperform the techniques in the available literature in terms of amplitude and aliasing distortion, reaching distortion around 2.4489 × 10 and 3.4907 × 10, respectively. This optimization algorithm's usefulness is further demonstrated with the sub-band coding of ECG signals Implementing optimal prototype filters has tangible real-world effects, especially in critical sectors like healthcare and communications, improving diagnostics accuracy, data transmission efficiency, and overall performance
PubMed: 38841468
DOI: 10.1016/j.heliyon.2024.e31912