Fraction Of Samples Research Articles

Differential Gene Expression Analysis of Whole Blood Transcriptome Between Young and Old Border Collie Dogs

Aging is the most significant risk factor for many diseases and increased mortality, and it is influenced by both genetic and environmental factors. In this study, our primary goal was to investigate age-related gene expression changes in whole blood samples collected from dogs and identify potential biomarkers of healthy aging. We sequenced the mRNA fraction of whole blood samples from five young and five old border collie dogs and performed differential gene expression and differential transcript usage analyses. The raw sequencing data exhibited high quality. Multidimensional scaling analysis failed to differentiate age clusters. Moreover, we identified only a limited number of differentially expressed genes (n = 61) and 30 genes with differential transcript usage between the blood transcriptomes of young and old dogs. Our results align with publicly available data on dogs. However, studies on other species, such as wolves, have identified more significant age-related genes. In conclusion, while some of our findings are promising, further research is needed to standardize environmental factors affecting blood gene expression levels in dogs. Additionally, we recommend implementing pre-sequencing hemoglobin depletion to improve the analysis of whole blood in future studies.

Gel-Based Sample Fractionation with SP3-Purification for Top-Down Proteomics.

Precise prefractionation of proteome samples is a potent method for realizing in-depth analysis in top-down proteomics. PEPPI-MS (Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS), a gel-based sample fractionation method, enables high-resolution proteome fractionation based on molecular weight by highly efficient extraction of proteins from polyacrylamide gels after SDS-PAGE separation. Thereafter it is essential to effectively remove contaminants such as CBB and SDS from the PEPPI fraction prior to mass spectrometry. In this study, we developed a complete, robust, and simple sample preparation workflow named PEPPI-SP3 for top-down proteomics by combining PEPPI-MS with the magnetic bead-based protein purification approach used in SP3 (single-pot, solid-phase-enhanced sample preparation), now one of the standard sample preparation methods in bottom-up proteomics. In PEPPI-SP3, proteins extracted from the gel are collected on the surface of SP3 beads, washed with organic solvents, and recovered intact with 100 mM ammonium bicarbonate containing 0.05% (w/v) SDS. The recovered proteins are subjected to mass spectrometry after additional purification using an anion-exchange StageTip. Performance validation using human cell lysates showed a significant improvement in low-molecular-weight protein recovery with a lower coefficient of variation compared to conventional PEPPI workflows using organic solvent precipitation or ultrafiltration.

Glacial dispersal of indicator minerals from the Brazil Lake LCT pegmatites, southwest Nova Scotia, Canada

The Brazil Lake lithium-cesium-tantalum (LCT)-type pegmatites (North, South, and Army Road pegmatites) in eastern Canada, were the focus of a detailed till study to document glacial dispersal of LCT pegmatite indicator minerals from bedrock. A total of 84 bulk (7-20 kg) till samples were collected from 77 sites around and down ice of the three pegmatites. The <2.0 mm fraction of the till samples was processed using shaking table and heavy liquid methods to produce 2.8-3.2 and >3.2 specific gravity (SG) non-ferromagnetic heavy mineral concentrates for visual identification and counting of indicator minerals in the 0.25-0.5 mm, 0.5-1.0 mm and 1-2 mm fractions. Glacial dispersal from the pegmatites is best defined by spodumene (the primary ore mineral) in the 0.25-0.5 mm fraction of the 2.8-3.2 SG concentrates, and its presence in the till (100s to 1000s of grains per sample) is visual confirmation of the existence of nearby LCT pegmatites. Glacial dispersal of spodumene forms a fan-shaped exploration target 12 km down ice that is considerably larger than the pegmatite subcrop areas. Other useful LCT pegmatite indicator minerals in the local till include apatite and tourmaline (10s to 100s of grains) and lesser amounts of columbite-tantalite, cassiterite, and scheelite (1s to 10s of grains), however, their abundances and spatial distributions are much less/smaller than that for spodumene. The results clearly demonstrate that indicator mineral methods are useful for Li exploration in the glaciated terrains of southwest Nova Scotia, across Canada, and other prospective glaciated terrains globally.

Quantitative proteomic analysis unveils a critical role of VARS1 in hepatocellular carcinoma aggressiveness through the modulation of MAGI1 expression

BackgroundHepatocellular carcinoma (HCC) genetic/transcriptomic signatures have been widely described. However, its proteomic characterization is incomplete. We performed non-targeted quantitative proteomics of HCC samples and explored its clinical, functional, and molecular consequences.MethodsNon-targeted quantitative proteomics were performed on cytosolic and nuclear fractions of liver samples [HCC vs. non-tumour adjacent tissue (NTAT), n = 42 patients]. Changes were confirmed in 7 in silico HCC cohorts. Functional and molecular implications were evaluated on HCC-derived cell lines after silencing/overexpressing VARS1 and/or MAGI1. VARS1-overexpressing Hep3B cells were used for in vivo studies [Extreme Limiting Dilution Assay (ELDA) and orthotopic tumour formation]. Quantitative proteomics were performed on VARS1-overexpressing HCC cell lines.ResultsQuantitative proteomics revealed the dysregulation of the cytosolic and nuclear proteomes in HCC, and defined two proteomic HCC subgroups, the most aggressive associated to the dysregulation of the aminoacyl-tRNA synthetases (ARSs). ARSs dysregulation was corroborated in in silico HCC cohorts and associated to poor prognosis. Patients with ARSs upregulation had genomic/transcriptomic characteristics of the proliferative HCC. Valine tRNA-aminoacyl synthetase (VARS1) was the ARSs most consistently overexpressed and associated to aggressiveness. VARS1 modulation (silencing/overexpression) altered tumour establishment-associated parameters in vitro and/or in vivo. Quantitative proteomics on cells overexpressing VARS1 and rescue experiments identified the downregulation of MAGI1, a tumour suppressor in HCC, as a mediator of VARS1 function.ConclusionsQuantitative proteomics defines two prognosis-related proteomic HCC subgroups. ARSs machinery is dysregulated in the aggressive subgroup, bearing potential as prognostic biomarkers. VARS1 promotes aggressiveness through the modulation of MAGI1, representing a novel targetable vulnerability in HCC.

DEVELOPMENT AND VALIDATION OF A METHODOLOGY FOR QUANTIFICATION OF WHEY PROTEIN FRACTIONS IN MICROPARTICULATE INGREDIENTS

Microparticulated whey protein can be used as a fat substitute in foods to enhance their nutritional value and improve their sensory and rheological characteristics. Microparticulation denatures whey proteins through heat treatment, followed by shear rate control to determine the aggregate sizes formed. The processing method used during microparticulation can modify the protein denaturation rate, which may enable the application of new proteins. This study sought to develop a methodology for quantifying whey protein fractions in commercial samples before and after microparticulation at different concentrations and physical states. The developed methodology proved to be applicable because of its selectivity, quantification, detection limits, and precision. The analyzed samples exhibited a higher denaturation rate for β-lactoglobulin than α-lactoalbumin; the denaturation rate varied among samples due to differences in the microparticulation process.

Structural Bifurcation in the High→Low‐Spin and Low→High‐Spin Phase Transitions Explains the Asymmetric Spin‐Crossover in [FeL2][BF4]2 (L=2,6‐Di{pyrazol‐1‐yl}isonicotinonitrile)

AbstractPolycrystalline [FeL2][BF4]2 (L=2,6‐di(pyrazol‐1‐yl)isonicotinonitrile) exhibits an abrupt hysteretic spin transition near 240 K, with a shoulder on the warming branch whose appearance depends on the sample history. The freshly isolated material is a ca 60 : 40 mixture of triclinic (HS1) and tetragonal (HS2) high‐spin polymorphs, which are structurally closely related. Both HS1 and HS2 undergo a high→low‐spin transition on cooling at 230±10 K. HS1 transforms to a new triclinic low‐spin phase with a doubled unit cell volume (LS3), while HS2 forms a monoclinic low‐spin phase (LS4) with similar unit cell dimensions to HS2. Single crystals of LS3 and LS4 both convert to HS1 on rewarming. The low→high‐spin transition for LS4 is ca 10 K higher in temperature than for LS3, explaining the asymmetric thermal hysteresis. Powder diffraction, calorimetry and magnetic data show that multiple cycling about the spin‐transition leads to slow enrichment of the HS1 and LS3 phases at the expense of HS2 and LS4. That is consistent with the HS2/LS4 fraction of the polycrystalline sample undergoing rare, bifurcated HS2→(LS3+LS4) and LS4→(HS1+HS2) phase transitions. The rate of enrichment of HS1/LS3 differed between these experiments, implying it is sample and/or measurement‐dependent. Three other salts of this iron(II) complex and the coordination polymer [Ag(μ‐L)]BF4 are also briefly described.

Structural Bifurcation in the High→Low-Spin and Low→High-Spin Phase Transitions Explains the Asymmetric Spin-Crossover in [FeL2][BF4]2 (L=2,6-Di{pyrazol-1-yl}isonicotinonitrile).

Polycrystalline [FeL2][BF4]2 (L=2,6-di(pyrazol-1-yl)isonicotinonitrile) exhibits an abrupt hysteretic spin transition near 240 K, with a shoulder on the warming branch whose appearance depends on the sample history. The freshly isolated material is a ca 60 : 40 mixture of triclinic (HS1) and tetragonal (HS2) high-spin polymorphs, which are structurally closely related. Both HS1 and HS2 undergo a high→low-spin transition on cooling at 230±10 K. HS1 transforms to a new triclinic low-spin phase with a doubled unit cell volume (LS3), while HS2 forms a monoclinic low-spin phase (LS4) with similar unit cell dimensions to HS2. Single crystals of LS3 and LS4 both convert to HS1 on rewarming. The low→high-spin transition for LS4 is ca 10 K higher in temperature than for LS3, explaining the asymmetric thermal hysteresis. Powder diffraction, calorimetry and magnetic data show that multiple cycling about the spin-transition leads to slow enrichment of the HS1 and LS3 phases at the expense of HS2 and LS4. That is consistent with the HS2/LS4 fraction of the polycrystalline sample undergoing rare, bifurcated HS2→(LS3+LS4) and LS4→(HS1+HS2) phase transitions. The rate of enrichment of HS1/LS3 differed between these experiments, implying it is sample and/or measurement-dependent. Three other salts of this iron(II) complex and the coordination polymer [Ag(μ-L)]BF4 are also briefly described.

Evaluating the Efficiency of Dust Stone as an Improvement Material for Cement Gravel Column

This research explores the feasibility of incorporating dust stone into cement gravel columns to enhance their mechanical properties and sustainability profile. A series of laboratory experiments including unconfined compressive strength (UCS) and permeability tests were carried out. 15 mixture designs were prepared to investigate the effect of stone dust (5-20% of cement and 0, 5, 10, 15, and 20% by weight of highest porous sample) on volume fractions of CG samples on engineering and physical properties of cemented gravel samples, at 7 and 28 days. The findings indicate that the ideal proportion of stone dust is 10%, which significantly enhances the compressibility of the CG mixture while preserving satisfactory permeability. The finding indicates that stone dust is a feasible and efficient additive for improving the performance of cement gravel columns in civil engineering applications. Moreover, stone dust provides sustainability advantages by minimizing waste production and contributing to a circular economy.

G.O.Joe: A new non‐commercial software tool for the processing of LA‐ICP‐MS trace element data

A common problem of trace element measurements by LA‐ICP‐MS is the existence of interferences that cannot be resolved instrumentally. The software G.O.Joe is developed to calculate trace element mass fractions in solid samples analysed by LA‐ICP‐MS, offering the opportunity to correct for isobaric interference (including mass bias) and abundance sensitivity. Designed as a platform‐independent web application, G.O.Joe is written in the Dart programming language and runs on all web browsers supported by Flutter (i.e., Chrome, Safari, Edge, Firefox) without the need for installation. G.O.Joe is freely accessible from any computer with an internet connection to facilitate immediate data evaluation and the efficient processing of large datasets (> 400 analyses). G.O.Joe features an intuitive user interface that simplifies the selection of peak and background signals, import of instrument settings and reference material compositions to convert the measured raw signals into element mass fractions. Key functions of G.O.Joe are presented by processing the analysis of tungstates and silicates (i.e., scheelite and garnet) including specific correction methods to demonstrate their large effect on interfered masses/isotopes achievable with only little effort. This study introduces G.O.Joe as a simple, time‐efficient and flexible software to significantly improve data quality in various trace element studies utilising LA‐ICP‐MS.

The reliability of gas-phase metallicities immediately adjacent to non-star-forming spaxels in MaNGA

Abstract In this work, we use gas phase metallicities calculated from the Sloan Digital Sky Survey (SDSS) Mapping Nearby Galaxies at Apache Point (MaNGA) Data Release 17 (DR17) to assess the extent of potential biases in spaxels which are spatially adjacent to spaxels identified as non-star forming (non-SF) on a BPT diagram. We identify a sample of ∼21, 000 such spaxels with calculable metallicities from the full metallicity catalogue (∼1.57 million), representing a small fraction (∼1.3 per cent) of the full metallicity sample. ∼23 per cent of all galaxies with at least one spaxel with a calculable metallicity also contain at least one spaxel with a calculated metallicity adjacent to a non-SF spaxel, with a typical galaxy hosting 9 non-SF-adjacent spaxels. From our suite of 6 different metallicity calibrations, we find that only the metallicity calibrations based entirely on the [N ii]6584/Hα ratio are affected, showing systematic offsets to higher metallicities by up to ∼0.04 dex if they are located adjacent to a non-SF flagged spaxel, relative to a radially matched control sample. The inclusion of additional diagnostic diagrams (based on [O i]6300 &/or [S ii]6717 + 6731) is insufficient to remove the observed offset in the [N ii]6584/Hα based calibrations. Using a stricter diagnostic line on the BPT diagram removes ∼94 per cent of identified bordering spaxels with metallicities for all metallicity calibrations, and removes the residual offset to higher metallicity values seen in [N ii]6584/Hα calibrations. If science cases demand an exceptionally clean metallicity sample, we recommend either a stricter BPT cut, and/or a non-[N ii]6584/Hα based metallicity calibration.

Experimental and analytical investigation for mechanical behaviour of vegetable fiber reinforced concrete

The use of vegetable fibers in concrete has gained attention for enhancing material properties and promoting sustainable construction. This study evaluates the effects of three vegetable fibers—palm, luffa, and straw—on the mechanical properties of concrete, focusing on compressive, tensile, and flexural strengths. The experimental program varied the fiber types, lengths, and volume fractions in concrete samples. Results revealed that incorporating 1% palm fibers increased compressive strength by 1.6%, tensile strength by 2.7%, and flexural strength by 0.8% compared to plain concrete. Palm fibers cured in non-saline water exhibited the most notable improvements. In contrast, adding 1% luffa fibers resulted in approximately 10% increase in compressive strength but caused reductions in flexural (5.3%) and tensile (6%) strengths. Excessive fiber content adversely affected strength due to increased moisture absorption and air content. A generalized self-consistent model confirmed the relationship between fiber content and the modulus of elasticity, while morphological analysis highlighted the anisotropic properties of palm fibers, suggesting their potential for optimizing concrete performance. This research underscores the suitability of palm fibers as cost-effective, eco-friendly alternatives to synthetic fibers, contributing to improved mechanical performance and sustainable management of agricultural waste.

Chemical Composition and Toxicity of Water-Soluble Fractions of Oil Samples from the Extensive Spill in Northeast Brazil.

This study evaluated the effects of water-soluble fractions (WSF) of stranded oil sampled from the beaches of Trancoso and Massarandupió (Bahia, Brazil) following a mysterious oil spill along Brazil's northeast coast (2019-2020). The samples were characterized for aliphatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs) and tested for chronic toxicity in the embryo-larval stages of the sea urchin Echinometra lucunter. The WSFs contained high levels of PAHs, some of which were above the acceptable levels for water in Brazil, and toxicity to sea urchin embryos tended to occur at higher concentrations.

Aged Lignocellulose Fibers of Cedar Wood (9th and 12th Century): Structural Investigation Using FTIR-Deconvolution Spectroscopy, X-Ray Diffraction (XRD), Crystallinity Indices, and Morphological SEM Analyses.

The characterization of lignocellulosic biomass present in archaeological wood is crucial for understanding the degradation processes affecting wooden artifacts. The lignocellulosic fractions in both the external and internal parts of Moroccan archaeological cedar wood (9th, 12th, and 21st centuries) were characterized using infrared spectroscopy (FTIR-ATR deconvolution mode), X-ray diffraction (XRD), and SEM analysis. The XRD demonstrates a significant reduction in the crystallinity index of cellulose from recent to aging samples. This finding is corroborated by the FTIR analysis, which shows a significant reduction in the area profiles of the C-H crystalline cellulosic bands (1374, 1315, and 1265 cm-1) and C-O-C (1150-1000 cm-1). The alterations in the lignin fraction of aging samples (from the 9th and 12th centuries) were demonstrated by a reduction in the intensity of the bands at 1271 and 1232 cm-1 (Car-O) and the formation of new compounds, such as quinones and/or diaryl carbonyl structures, within the 1700-1550 cm-1 range. The SEM images of cedar wood samples from the 9th and 12th centuries reveal voids, indicating that the entire cell wall component has been removed, a characteristic feature of simultaneous white rot fungi. In addition, horizontal "scratches" were noted, indicating possible bacterial activity.

Similar freezing spectra of particles in plant canopies and in the air at a high-altitude site

Abstract. Plant canopies are an important source of biological particles aerosolized into the atmosphere. Certain aerosolized microorganisms are able to freeze slightly supercooled cloud droplets and therefore affect mixed-phase cloud development. Still, spatiotemporal variability of such biological ice-nucleating particles (INPs) is currently poorly understood. Here, we study this variability between late summer and leaf shedding on the scale of individual leaves collected about fortnightly from four temperate broadleaf tree species (Fagus sylvatica, Juglans regia, Prunus avium and Tilia platyphyllos) on a hillside (Gempen, 650 m a.s.l. (metres above sea level)) and in a vertical canopy profile of one Fagus sylvatica (Hölstein, 550 m a.s.l.) in north-western Switzerland. The cumulative concentration of INPs active at ≥-10 °C (INPs−10) did not vary significantly between the investigated tree species but, as inferred from leaf mass per area and leaf carbon isotopic ratios, seemed to be lower on sun leaves as compared with shade leaves. Between August and mid-November, the median INP concentration increased from 4 to 38 INP−10 cm−2 of leaf area and was positively correlated with mean relative humidity throughout 24 h prior to sampling (Spearman's r=0.52, p<0.0001, n=64). In 53 of the total 64 samples collected at the Gempen site, differential INP spectra between −3 and −10 °C exhibited clearly discriminable patterns: in 53 % of the spectra, the number of additionally activated INPs increased persistently with each 1 °C decrease in temperature; the remaining spectra displayed significant peaks in differential INP concentration above −9 °C, most frequently in the temperature interval between −8 and −9 °C (21 %) and between −7 and −8 °C (17 %). Interestingly, the three most frequent patterns in differential INP spectra on leaves in Gempen were also prevalent in similar fractions in air samples with clearly discriminable patterns at the high-altitude Jungfraujoch site (3580 m a.s.l., Switzerland) collected during summer in the previous year. These findings corroborate the idea that a large fraction of the airborne biological INP population above the Alps during summer originates from plant surfaces. Which parameter or set of parameters could affect biological INP populations on both scales – upwind airsheds of high-altitude sites as well as individual leaves – is an intriguing question for further exploration. A first guess is that leaf wetness duration plays a role.

An assessment of Rare Earth Elements in borehole cores from the Ermelo, Witbank and Waterberg Coalfields, South Africa: Focus on mode of occurrence

There is currently limited knowledge concerning South African coal deposits as hosts for rare earth elements (REE). This project aims to determine the concentration of REE, including yttrium and scandium (REY+Sc) in various coal seams and adjacent sediments in borehole cores from the Ermelo, Witbank, and Waterberg coalfields in South Africa. Coal petrography (maceral count and vitrinite reflectance), XRD, XRF, sequential chemical extraction procedure (SCEP) before ICP-MS, and mineral liberation analysis (MLA) were conducted on the coal and associated sediment samples. The coals were inertinite-rich, medium-rank bituminous coal, with moderate to high ash content. The two dominant minerals in all the coalfields are kaolinite and quartz, except for sample ZBS2M, where dolomite was dominant. The dominant major oxides are Al2O3, SiO2, Fe2O3, and CaO, which concur with the XRD results. The ICP-MS results following SCEP indicated that both coal and the associated sediments were light REY+Sc dominant. There was also an elevation of medium REY+Sc in the Witbank coal's associated sediment samples. Notably, the samples with the highest REY+Sc results were the sediment samples. The Waterberg samples had the lowest REY+Sc from both the coal (less than 2 μg/g to 7 μg/g) and associated sediments (2 μg/g to 15 μg/g). While the highest REY+Sc was yielded from the Witbank-associated sediments (500 μg/g to 2,500 μg/g). The carbonate fraction step proved to be the most successful leaching step, as most REY+Sc was recovered in that step for all coalfields. In addition to the carbonate fraction, the silicates and sulfide fraction in the Witbank samples, and the ion-exchangeable fraction for the Waterberg-associated sediments samples proved successful in leaching out the REY+Sc. MLA determined that monazite and xenotime in all the coal samples were the REY+Sc-bearing minerals.

A new Entoprocta species from the northwestern Weddell Sea shelf (Southern Ocean), its soft-sediment habitat and possible polychaete hosts

Rare meiofauna taxa are often indicators of specific environmental conditions. A new and rare species of Entoprocta from the Southern Ocean, its abundance, habitat and possible commensal relationship with Polychaeta are presented. During the RV Polarstern expedition PS118 (2019) to the northwestern Weddell Sea, sediment samples were taken with a multicorer. The species of the family Loxosomatidae was discovered in the meiofauna size fraction of samples of only one of three investigated stations (413–415 m depth). Loxosomella sigridae sp. nov. is a solitary, medium-sized entoproct (total length up to 773 µm). Decisive characters of the adult include twelve tentacles, an aborally situated Y-shaped cell row, paired accessory gland cells along the foot groove and smooth adhesive papillae at the tip of the foot. The reproductive cycle of Loxosomella sigridae sp. nov. has a sexual and an asexual phase via larvae and bud-carrying individuals, respectively. We present confocal laser-scanning images of both developmental stages. Integrative methods are used to describe the habitat of Loxosomella sigridae sp. nov. and gain insight in its relationship to possible host organisms. We discuss co-occurring polychaete families and their ecology and conclude that Cirratulidae and/or Paraonidae may most likely be the hosts of Loxosomella sigridae sp. nov.

Studying Structural Details in Complex Samples. I. Combining two Chromatographic Separation Methods with Ultrahigh Resolution Mass Spectrometry.

The analysis of complex mixtures poses a challenge due to the high number of compounds present in a mixture, which often exceed the capabilities of analytical methods and instruments. Even more challenging is understanding the structural details of compounds within a complex sample. Most analytical methods provide just bulk information on complex samples, and individual structural details cannot be observed. High-resolution mass spectrometry, the best method to analyze complex samples, suffers from inherent problems for structural studies in complex systems because collision-induced fragmentation (CID) measurements cannot provide data from individual compounds alone. The combination of different steps of chromatographic separation, here the combination of size exclusion chromatography with argentation chromatography, provides sufficient reduction in complexity to implement a method that allows gaining structural details of individual compounds within a complex mixture. The combination of offline size exclusion chromatography followed by online argentation chromatography effectively creates fractions based on the respective properties of the compounds in the mixture (size and number of π-bonds and heteroatoms) and reduces matrix effects to a great extent. Mass spectrometry with ultrahigh resolution provides basic chemical information for each detected compound and also provides the opportunity to gain structural information from MS/MS experiments. The results indicate effectively separated sample fractions yielded by the chromatographic steps with tremendously decreased total numbers of compounds. Especially, argentation chromatography proved to be a valuable separation tool when it comes to heteroatom-containing constituents. In the end, the fragmentation experiments indicated high-quality data due to the clean ion isolation enabled by prior separation. The structural elucidations provided deep insights into the carbon space of crude oil.

Analysis and fully memristor-based reservoir computing for temporal data classification

Reservoir computing (RC) offers a neuromorphic framework that is particularly effective for processing spatiotemporal signals. Known for its temporal processing prowess, RC significantly lowers training costs compared to conventional recurrent neural networks. A key component in its hardware deployment is the ability to generate dynamic reservoir states. Our research introduces a novel dual-memory RC system, integrating a short-term memory via a WOx-based memristor, capable of achieving 16 distinct states encoded over 4 bits, and a long-term memory component using a TiOx-based memristor within the readout layer. We thoroughly examine both memristor types and leverage the RC system to process temporal data sets. The performance of the proposed RC system is validated through two benchmark tasks: isolated spoken digit recognition and with only a fraction of complete samples forecasting the Mackey-Glass (MG) time series prediction. The system delivered an impressive 98.84% accuracy in speech digit recognition and sustained a low normalized root mean square error (NRMSE) of 0.036 in the time series prediction task, underscoring its capability. This study illuminates the adeptness of memristor-based RC systems in managing intricate temporal challenges, laying the groundwork for further innovations in neuromorphic computing.

Comprehensive evaluation of the impact of whole-genome bisulfite sequencing (WGBS) on the fragmentomic characteristics of plasma cell-free DNA

BackgroundCell-free DNA (cfDNA) is non-randomly fragmented in human body fluids. Analyzing such fragmentation patterns of cfDNA holds great promise for liquid biopsy. Whole-genome bisulfite sequencing (WGBS) is widely used for cfDNA methylation profiling. However, its applicability for studying fragmentomic characteristics remains largely unexplored. MethodsWe performed paired WGBS and whole-genome sequencing (WGS) on 66 peripheral plasma samples from 58 pregnant women. Then, we systematically compared the fragmentation patterns of cell-free nuclear DNA and mitochondrial DNA (mtDNA) sequenced from these two approaches. Additionally, we evaluated the extent of the size shortening in fetal-derived cfDNA and estimated the fetal DNA fraction in maternal plasma using both sequencing methods. ResultsCompared to WGS samples, WGBS samples demonstrated a significantly lower genome coverage and higher GC content in cfDNA. They also showed a significant decrease in the size of cell-free nuclear DNA, along with alterations in the end motif pattern that were specifically associated with CpG and “CC” sites. While there was a slight shift in the inferred nucleosome footprint from cfDNA coverages in WGBS samples, the cfDNA coverage patterns in CTCF and TSS regions remained highly consistent between these two sequencing methods. Both methods accurately reflected gene expression levels through their TSS coverages. Additionally, WGBS samples exhibited an increased abundance and longer length of mtDNA in plasma. Furthermore, we observed the size shortening of fetal cfDNA in plasma consistently, with a highly correlated fetal DNA fraction inferred by cfDNA coverage between WGBS and WGS samples (r = 0.996). However, the estimated fetal cfDNA fraction in WGBS samples was approximately 7 % lower than in WGS samples. ConclusionsWe confirmed that WGBS can introduce artificial breakages to cfDNA, leading to altered fragmentomic patterns in both nuclear and mitochondrial DNA. However, WGBS cfDNA remains suitable for analyzing certain cfDNA fragmentomic characteristics, such as coverage in genome regulation regions and the essential characteristics of fetal DNA in maternal plasma.

Proteomic analysis of the human amniotic mesenchymal stromal cell secretome by integrated approaches via filter-aided sample preparation

The immunomodulatory, anti-inflammatory and regenerative properties of the human amniotic mesenchymal stromal cells (hAMSCs) secretome are acknowledged but the understanding of the specific bioactive components remains incomplete. To address these limitations, the present investigation aimed to profile the proteins and peptides content of the hAMSC secretome through sample pretreatment and fractionation on 10 kDa molecular cut-off FASP (Filter Aided Sample Preparation) device and LC-MS analysis. The filter retained protein fraction underwent trypsin digestion, while the unretained was collected unchanged for intact small proteins and peptides analysis. This combined approach (C-FASP) collects in a single step two complementary fractions, advantageously saving sample volume and time of analysis. The bottom-up analysis of the C-FASP proteins fraction >10 kDa confirmed our previous findings, establishing a set of proteins consistently characterizing the hAMSC secretome. The analysis of the fraction <10 kDa, never been investigated to our knowledge, identified peptide fragments of thymosin beta 4 and beta 10, collagen alpha 1 chains I and III, alpha-enolase, and glyceraldehyde-3-phosphate dehydrogenase, involved in wound healing, anti-inflammatory response, tissue repair and regeneration, key biological activities of the secretome. C-FASP provided a comprehensive molecular profile of the hAMSC secretome offering new insights for enhanced therapeutic applications in regenerative medicine. SignificanceIn this investigation we originally present the comprehensive proteomic investigation of the human amniotic mesenchymal stromal cell secretome by combining the analysis of the proteome and of the peptidome following sample pretreatment and fractionation by Filter Aided Sample Preparation (FASP) with 10 kDa molecular cut-off in coupling with LC-MS analysis. The proteome fraction retained by FASP filter was analyzed after enzymatic digestion, while the unretained fraction, below 10 kDa molecular mass, was analyzed unchanged in its intact form. This dual approach provides novel insights, previously unexplored, into the molecular components potentially responsible for the immunomodulatory and anti-inflammatory properties of the hAMSC secretome. These findings could significantly enhance the therapeutic potential of hAMSCs in regenerative medicine.