Main Signatures Research Articles

Identification of a Novel β-Defensin Gene in Gilthead Seabream (Sparus aurata).

The excessive use of antibiotics in aquaculture favors the natural selection of multidrug-resistant bacteria, and antimicrobial peptides (AMPs) could be a promising alternative to this problem. The most studied AMPs in teleost fish are piscidins, hepcidins, and β-defensins. In this work, we have found a new gene (defb2) encoding a type 2 β-defensin in the genome of gilthead seabream, a species chosen for its economic interest in aquaculture. Its open reading frame (192bp) encodes a protein (71 amino acids) that undergoes proteolytic cleavage to obtain the functional mature peptide (42 amino acids). The genetic structure in three exons and two introns and the six characteristic cysteines are conserved as the main signature of this protein family. In the evolutionary analysis, synteny shows a preservation of chromosomal localization and the phylogenetic tree constructed exposes the differences between both types of β-defensin as well as the similarities between seabream and European seabass. In relation to its basal expression, β-defensin 2 is mostly expressed in the intestine, thymus, skin, and gonads of the gilthead seabream (Sparus aurata). In head kidney leucoytes (HKLs), the expression was very low and did not change significantly when stimulated with various immunocompetent agents. However, the expression was significantly down-regulated in the liver, head-kidney, and blood 4h post-injection with the fish pathogen Vibrio harveyi. When infected with nodavirus, the expression was downregulated in brain at 7days post-infection. These results denote a possible complementarity between the expression patterns of β-defensins and hepcidins. Further studies are needed to analyze gene duplications and expression patterns of β-defensins and describe their mechanism of action in seabream and other teleost fish.

G band enhancement in ABt-twisted trilayer graphene

G band, originating from the in-plane vibrations of carbon atoms, is the main signature in Raman spectroscopy of graphene-based systems. It is often used to characterize the sample quality and obtain molecular vibration information. Here we investigate the Raman spectroscopy of ABt-twisted trilayer graphene (ABt-TTG) and observe two enhancement centers for the G band across samples with different twist angles. To understand the origin of these two enhancement centers, we theoretically calculate the G band intensity of ABt-TTG based on the continuum model. We find that the theoretical calculations exhibit two prominent peaks corresponding to the experimental observations after Fermi velocity corrections. We also investigated the real and imaginary parts of Raman resonances, respectively, and explained the origins of two enhancements of ABt-TTG. By using Raman spectroscopy, evolutions of band structures of ABt-TTG with respect to the twist angles can be characterized, which extends the potential applications of the Raman method in the investigation of electronic structures of graphene-based systems.

Advances, recognition, and interpretation of molecular heterogeneity among conventional and subtype histology of urothelial carcinoma (UC): a survey among urologic pathologists and comprehensive review of the literature.

Urothelial carcinoma (UC) demonstrates significant molecular and histologic heterogeneity. The WHO 2022 classification has hinted at adding molecular signatures to the morphologic diagnosis. As morphology and associated molecular repertoire may potentially translate to choices of and response to therapy and relapse rate, broader acceptability of recognizing these key features among uropathologists is needed. This prompted an international survey to ascertain the practice patterns in classical/subtype UC among uropathologists across the globe. A survey instrument was shared among 98 uropathologists using SurveyMonkey software. Anonymized respondent data were analysed. The response rate was 85%. A majority were in concordance with the profiles of luminal (93%) and basal (82%) types. Opinion on the FGFR3 testing platform was variable. While 95% concurred that TERT promoter mutation is the key driver in UC, 72% had the opinion that APOBEC mutagenesis is the main signature in muscle invasive bladder cancer (MIBC). Uropathologists have divergent opinions on MIBC and ERCC2 mutations. Among the participants, 94% would quantify aggressive micropapillary and sarcomatoid histology, while 88% would reevaluate another transurethral resection of the bladder tumour specimen in nonmuscle invasive tumour with micropapillary, small cell, or sarcomatoid histology. A leading number agreed to specific molecular signatures of micropapillary (93%), plasmacytoid (97%), and small cell (86%) subtypes. Ninety-six percent of participants agreed that a small-cell component portends a more aggressive course and should be treated with neoadjuvant chemotherapy and 63% would perform HER2/neu testing only on oncologist's request in advanced tumours. Ninety percent agreed that microsatellite instability testing, although not a standard protocol, should be considered in young patients with upper tract UC. Eighty-six percent agreed that UC with high tumour mutational burden would be a better candidate for immunotherapy. In the era of precision medicine, enhanced understanding of molecular heterogeneity of UC will contribute to better therapeutic options, novel biomarker discovery, innovative management protocols, and outcomes. Our survey provides a broad perspective of pathologists' perceptions and experience regarding incorporation of histomolecular approaches to "personalize" therapy. Due to variable clinical adoption, there is a need for additional data using uniform study criteria. This will drive generation of best practice guidelines in this area for widespread and consistent clinical utility.

The Gaia-ESO Survey: No sign of multiple stellar populations in open clusters from their sodium and oxygen abundances

Context. The light element (anti-)correlations shown by globular clusters (GCs) are the main spectroscopic signature of multiple stellar populations. These internal abundance variations provide us with fundamental constraints on the formation mechanism of stellar clusters. Aims. Using Gaia-ESO, the largest and most homogeneous survey of open clusters (OCs), we intend to check whether these stellar aggregates display the same patterns. Based on previous studies of many GCs, several young and massive clusters in the Magellanic Clouds, as well as a few OCs, we do not expect to find any anti-correlation, given the low mass of Milky Way OCs. Methods. We used the results based on UVES spectra of stars in Gaia-ESO to derive the distribution of Na and O abundances and see whether they show an unexplained dispersion or whether they are anti-correlated. By selecting only high-probability members with high-precision stellar parameters, we ended up with more than 700 stars in 74 OCs. We examined the O-Na distribution in 28 OCs with at least 4 stars available as well as the Na distribution in 24 OCs, with at least 10 stars available. Results. We find that the distribution of Na abundances is compatible with a single-value population, within the errors. The few apparent exceptions can be explained by differences in the evolutionary phase (main sequence and giant post first dredge-up episode) or by difficulties in analysing low gravity giants. We did not find any indication of an Na-O anti-correlation in any of the clusters for which O has been derived. Conclusions. Based on the very small spread we find, OCs maintain the status of single stellar populations. However, a definitive answer requires studying more elements and larger samples covering different evolutionary phases. This will be possible with the next generation of large surveys.

Dissipative Soliton Resonance: Adiabatic Theory and Thermodynamics

We present the adiabatic theory of dissipative solitons (DS) of complex cubic-quintic nonlinear Ginzburg–Landau equation (CQGLE). Solutions in the closed analytical form in the spectral domain have the shape of Rayleigh–Jeans distribution for a positive (normal) dispersion. The DS parametric space forms a two-dimensional (or three-dimensional for the complex quintic nonlinearity) master diagram connecting the DS energy and a universal parameter formed by the ratio of four real and imaginary coefficients for dissipative and non-dissipative terms in CQGLE. The concept of dissipative soliton resonance (DSR) is formulated in terms of the master diagram, and the main signatures of transition to DSR are demonstrated and experimentally verified. We show a close analogy between DS and incoherent (semicoherent) solitons with an ensemble of quasi-particles confined by a collective potential. It allows applying the thermodynamical approach to DS and deriving the conditions for the DS energy scalability.

Custodial symmetry breaking and Higgs boson signatures at the LHC

We discuss the simplest model that predicts a tree-level modification of the ρ parameter from a shift in the W-mass without changing the prediction for the Z mass. This model predicts a new neutral Higgs and two charged Higgses, with very similar masses and suppressed couplings to the Standard Model fermions. We discuss the decay properties of these new scalar bosons, and the main signatures at the Large Hadron Collider. Comparing these signatures for the first time to the latest measurements, we show that while masses around 200 GeV are excluded for some scenarios, over a wide range of model parameter space the new bosons can have a mass close to the electroweak scale without violating existing limits from experimental searches or destroying the agreement with measurements. We investigate the scenario where the new neutral Higgs is fermiophobic and has a large branching ratio into W gauge bosons and/or photons, and show that this could lead to a signal in the diphoton mass spectrum at low Higgs masses. We discuss the different signatures that can motivate new measurements and searches at the Large Hadron Collider. Published by the American Physical Society 2024

Identification of Early Hippocampal Dynamics during Recognition Memory with Independent Component Analysis.

The hippocampus is generally considered to have relatively late involvement in recognition memory, its main electrophysiological signature being between 400 and 800 ms after stimulus onset. However, most electrophysiological studies have analyzed the hippocampus as a single responsive area, selecting only a single-site signal exhibiting the strongest effect in terms of amplitude. These classical approaches may not capture all the dynamics of this structure, hindering the contribution of other hippocampal sources that are not located in the vicinity of the selected site. We combined intracerebral electroencephalogram recordings from epileptic patients with independent component analysis during a recognition memory task involving the recognition of old and new images. We identified two sources with different responses emerging from the hippocampus: a fast one (maximal amplitude at ∼250 ms) that could not be directly identified from raw recordings and a latter one, peaking at ∼400 ms. The former component presented different amplitudes between old and new items in 6 out of 10 patients. The latter component had different delays for each condition, with a faster activation (∼290 ms after stimulus onset) for recognized items. We hypothesize that both sources represent two steps of hippocampal recognition memory, the faster reflecting the input from other structures and the latter the hippocampal internal processing. Recognized images evoking early activations would facilitate neural computation in the hippocampus, accelerating memory retrieval of complementary information. Overall, our results suggest that the hippocampal activity is composed of several sources with an early activation related to recognition memory.

Multi-omics subgroups associated with glycaemic deterioration in type 2 diabetes: an IMI-RHAPSODY Study.

Type 2 diabetes (T2D) onset, progression and outcomes differ substantially between individuals. Multi-omics analyses may allow a deeper understanding of these differences and ultimately facilitate personalised treatments. Here, in an unsupervised "bottom-up" approach, we attempt to group T2D patients based solely on -omics data generated from plasma. Circulating plasma lipidomic and proteomic data from two independent clinical cohorts, Hoorn Diabetes Care System (DCS) and Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS), were analysed using Similarity Network Fusion. The resulting patient network was analysed with Logistic and Cox regression modelling to explore relationships between plasma -omic profiles and clinical characteristics. From a total of 1,134 subjects in the two cohorts, levels of 180 circulating plasma lipids and 1195 proteins were used to separate patients into two subgroups. These differed in terms of glycaemic deterioration (Hazard Ratio=0.56;0.73), insulin sensitivity and secretion (C-peptide, p=3.7e-11;2.5e-06, DCS and GoDARTS, respectively; Homeostatic model assessment 2 (HOMA2)-B; -IR; -S, p=0.0008;4.2e-11;1.1e-09, only in DCS). The main molecular signatures separating the two groups included triacylglycerols, sphingomyelin, testican-1 and interleukin 18 receptor. Using an unsupervised network-based fusion method on plasma lipidomics and proteomics data from two independent cohorts, we were able to identify two subgroups of T2D patients differing in terms of disease severity. The molecular signatures identified within these subgroups provide insights into disease mechanisms and possibly new prognostic markers for T2D.

Verification of ultrafast spin transfer effects in iron-nickel alloys

The optical intersite spin transfer (OISTR) effect was recently verified in Fe50Ni50 using extreme ultraviolet magneto-optical Kerr measurements. However, one of the main experimental signatures analyzed in this work, namely a magnetic moment increase at a specific energy in Ni, was subsequently found also in pure Ni, where no transfer from one element to another is possible. Hence, it is a much-discussed issue whether OISTR in FeNi alloys is real and whether it can be verified experimentally or not. Here, we present a comparative study of spin transfer in Fe50Ni50, Fe19Ni81 and pure Ni. We conclusively show that an increase in the magneto-optical signal is indeed insufficient to verify OISTR. However, we also show how an extended data analysis overcomes this problem and allows to unambiguously identify spin transfer effects. Concomitantly, our work solves the long-standing riddle about the origin of delayed demagnetization behavior of Ni in FeNi alloys.

A chemodynamical analysis of bright metal-poor stars from the HESP-GOMPA survey – indications of a non-prevailing site for light r-process elements

ABSTRACT We present a comprehensive analysis of the detailed chemical abundances for a sample of 11 metal-poor, very metal-poor, and extremely metal-poor stars ([Fe/H] = −1.65 to [Fe/H] = −3.0) as part of the HESP-GOMPA (Galactic survey Of Metal Poor stArs) survey. The abundance determinations encompass a range of elements, including C, Na, Mg, Al, Si, Ca, Sc, Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn, Sr, and Ba, with a subset of the brighter objects allowing for the measurement of additional key elements. Notably, the abundance analysis of a relatively bright highly r-process-enhanced (r-II) star (SDSS J0019+3141) exhibits a predominantly main r-process signature and variations in the lighter r-process elements. Moreover, successful measurements of thorium in this star facilitate stellar age determinations. We find a consistent odd–even nucleosynthesis pattern in these stars, aligning with expectations for their respective metallicity levels, thus implicating Type II supernovae as potential progenitors. From the interplay between the light and heavy r-process elements, we infer a diminishing relative production of light r-process elements with increasing Type II supernova contributions, challenging the notion that Type II supernovae are the primary source of these light r-process elements in the early Milky Way. A chemodynamical analysis based on Gaia astrometric data and our derived abundances indicates that all but one of our program stars are likely to be of accreted origin. Additionally, our examination of α-poor stars underscores the occurrence of an early accretion event from a satellite on a prograde orbit, similar to that of the Galactic disc.

Proteomics of serum-derived extracellular vesicles are associated with the severity and different clinical profiles of patients with COVID-19: An exploratory secondary analysis

Coronavirus disease 2019 (COVID-19) is characterized by a broad spectrum of clinical manifestations with the potential to progress to multiple organ dysfunction in severe cases. Extracellular vesicles (EVs) carry a range of biological cargoes, which may be used as biomarkers of disease state. An exploratory secondary analysis of the SARITA-2 and SARITA-1 datasets (randomized clinical trials on patients with mild and moderate/severe COVID-19) was performed. Serum-derived EVs were used for proteomic analysis to identify enriched biological processes and key proteins, thus providing insights into differences in disease severity. Serum-derived EVs were separated from patients with COVID-19 by size exclusion chromatography and nanoparticle tracking analysis was used to determine particle concentration and diameter. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed to identify and quantify protein signatures. Bioinformatics and multivariate statistical analysis were applied to distinguish candidate proteins associated with disease severity (mild versus moderate/severe COVID-19). No differences were observed in terms of the concentration and diameter of enriched EVs between mild (n = 14) and moderate/severe (n = 30) COVID-19. A total of 414 proteins were found to be present in EVs, of which 360 were shared while 48 were uniquely present in severe/moderate compared to mild COVID-19. The main biological signatures in moderate/severe COVID-19 were associated with platelet degranulation, exocytosis, complement activation, immune effector activation, and humoral immune response. Von Willebrand factor, serum amyloid A-2 protein, histone H4 and H2A type 2-C, and fibrinogen β-chain were the most differentially expressed proteins between severity groups. Exploratory proteomic analysis of serum-derived EVs from patients with COVID-19 detected key proteins related to immune response and activation of coagulation and complement pathways, which are associated with disease severity. Our data suggest that EV proteins may be relevant biomarkers of disease state and prognosis.

Соматическая лексика Веспасиановой Псалтири

The article focuses on the linguistic properties of Old English somatic vocabulary represented by the specific lexis and idiomatic expressions collected from The Vespasian Psalter, an 8 th century Anglo-Saxon glossed manuscript. The research submits to scrutiny 37 substantive words with corporeal semantics, which are grouped according to the conventional procedure. In the text of the Vespasian Psalter 750 contexts with lexical somatisms are thoroughly analyzed to calculate the frequency of occurrence of each unit and detect the corporeal vocabulary which enjoys the highest frequency and therefore may prove to be phraseologically productive. Proceeding from the analysis of a number of contexts with the noun toð (tooth), the study is made of the capacity of lexical somatisms to build regular idiomatic complexes with the contextual ambience. The emphasis is laid on the fact that the main signatures of idiomatization are regular speech incidence of the somatic component combined with certain words and a constant image underpinning the semantic structure of the hereby formed idiomatic word-combination. To verify the phraseological status of the word-combinations, contexts are considered in comparison with the corresponding contexts in other Old English manuscripts. The research can be of interest to specialists in a number of linguistic departments: lexicology, phraseology, linguoculturology and history of English.

Single-cell RNA sequencing reveals heterogeneity and differential expression of the maternal–fetal interface during ICP and normal pregnancy

Objective Intrahepatic cholestasis of pregnancy (ICP) can cause adverse perinatal outcomes. Previous studies have demonstrated that the placenta of an ICP pregnancy differs in morphology and gene expression from the placenta of a normal pregnancy. To date, however, the genetic mechanism by which ICP affects the placenta is poorly understood. Therefore, the aim of this study was to investigate the differences in main cell types, gene signatures, cell ratio, and functional changes in the placenta between ICP and normal pregnancy. Methods Single-cell RNA sequencing (scRNA-seq) technology was used to detect the gene expression of all cells at the placental maternal–fetal interface. Two individuals were analyzed – one with ICP and one without ICP. The classification of cell types was determined by a graph-based clustering algorithm. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the R software phyper () function and DAVID website. The differentially expressed genes (DEGs) encoding transcription factors (TFs) were identified using getorf and DIAMOND software. Results We identified 14 cell types and 22 distinct cell subtypes that showed unique functional properties. Additionally, we found differences in the proportions of fibroblasts 1, helper T (Th) cells, extravillous trophoblasts, and villous cytotrophoblasts, and we observed heterogeneity of gene expression between ICP and control placentas. Furthermore, we identified 263 DEGs that belonged to TF families, including zf-C2H2, HMGI/HMGY, and Homeobox. In addition, 28 imprinted genes were preferentially expressed in specific cell types, such as PEG3 and PEG10 in trophoblasts as well as DLK1 and DIO3 in fibroblasts. Conclusions Our results revealed the differences in cell-type ratios, gene expression, and functional changes between ICP and normal placentas, and heterogeneity was found among cell subgroups. Hence, the imbalance of various cell types affects placental activity to varying degrees, indicating the complexity of the cell networks that form the placental tissue system, and this alteration of placental function is associated with adverse events in the perinatal period.

(Invited) Plasma-Synthesized Coupled Nanoplasmonic Gold for DNA Sersing

The facilitated electrochemical properties of plasma play a critical role in enhancing the synthesis and design of functional nanomaterials for the development of novel sensors. The targeted challenge is to customize and tailor functionality at multiple scales to improve detection device performance. In the realm of optoelectronics, plasmonic sensing is considered an efficient tool for investigating molecular properties, often accompanied by Raman, FTIR or Fluorescent spectroscopy. Specifically, Raman scattering, also known as SERS (surface-enhanced Raman scattering), is commonly used to probe analytes at a reduced scale using plasmonic enhancers. This technique is especially useful for rapidly and accurately investigating biologically relevant samples, such as DNA and RNA. DNA/RNA-related investigations are crucial in modern nanomedicine due to the progress made in bionanotechnology, DNA vaccines, and functional gene engineering. DNA, in particular, is highly valued by microbiologists because it contains information about the nature of bio-species. Currently, PCR-related methods dominate the field for molecular-sensitive DNA-level studies, but it is challenging to investigate using optical techniques like SERS. Despite its promise, SERS still requires technological and analytical improvements. A sophisticated plasmonic nanomaterial provides considerably improved photon scattering due to the strongly localized field confinement effect, resulting in better performance. In this report, a nanoplasmonic sensor was designed using a plasma-driven electrochemical reduction mechanism, achieved through an atmospheric pressure He-plasma jet setup operating at kHz frequency. The reactive oxidative species donated electrons via liquid-gas electrochemistry towards the Ar-delivered Au(3+)-containing microdroplets, resulting in microscaled aggregates composed of AuNPs obtained from the nebulized ionic gold liquid precursor. Due to the strong coupling between nanoparticles, a high analytical enhancement factor of about 107 was achieved, and the substrate enabled obtaining Raman fingerprints of bacterial DNA fragments (M. luteus and S. aureus, E. coli, J. lividum) at nanovolume sample quantities. Additionally, the main DNA molecular vibrational signatures associated with nucleobase motions were extracted from the collected spectra and used to reliably classify bacterial strains using statistical principal component analysis.[1] References[1] Shvalya, V., Vasudevan, A., Modic, M., Abutoama, M., Skubic, C., Nadižar, N., ... & Cvelbar, U. (2022). Bacterial DNA Recognition by SERS Active Plasma-Coupled Nanogold. Nano Letters.

Fallopian tube lesions as potential precursors of early ovarian cancer: a comprehensive proteomic analysis

Ovarian cancer is the leading cause of death from gynecologic cancer worldwide. High-grade serous carcinoma (HGSC) is the most common and deadliest subtype of ovarian cancer. While the origin of ovarian tumors is still debated, it has been suggested that HGSC originates from cells in the fallopian tube epithelium (FTE), specifically the epithelial cells in the region of the tubal-peritoneal junction. Three main lesions, p53 signatures, STILs, and STICs, have been defined based on the immunohistochemistry (IHC) pattern of p53 and Ki67 markers and the architectural alterations of the cells, using the Sectioning and Extensively Examining the Fimbriated End Protocol. In this study, we performed an in-depth proteomic analysis of these pre-neoplastic epithelial lesions guided by mass spectrometry imaging and IHC. We evaluated specific markers related to each preneoplastic lesion. The study identified specific lesion markers, such as CAVIN1, Emilin2, and FBLN5. We also used SpiderMass technology to perform a lipidomic analysis and identified the specific presence of specific lipids signature including dietary Fatty acids precursors in lesions. Our study provides new insights into the molecular mechanisms underlying the progression of ovarian cancer and confirms the fimbria origin of HGSC.

Overview of a large observing campaign of Jupiter's aurora with the Hubble Space Telescope combined with Juno-UVS data

Between February and September 2019, Jupiter's ultraviolet aurorae were frequently observed during a large campaign of the Hubble Space Telescope (HST GO-15638). The campaign included approximately 10 visits around each of the perijoves of the Juno spacecraft orbits 18 to 22 around Jupiter. During this time, the solar activity was minimal, giving the opportunity to investigate auroral dynamics minimally driven by the solar wind. The main emission often appeared fainter than usually observed, particularly on the dawn side where the dawn arc was not always present. In contrast, emissions poleward of the main emission were dynamic, exhibiting polar bright spots, extremely bright flares and quasi-periodic flashes. Many other features are observed, such as dawn storms, long-standing secondary arc parallel to the main emission, injection signatures, transpolar arcs and bridges connecting the main emission to the polar emissions. HST high temporal and spatial resolutions enable the investigation of the dynamics of the auroral structures and substructures like beads within the main emission. Juno auroral observations are also combined with HST images to track conjugate auroral features in both hemispheres simultaneously. Finally, a splitting of the main emission into two narrow parallel arcs is highlighted for the first time.

WNMS: A New Basaltic Simulant of Mars Regolith

The use of planetary regolith can be explored via the utilization of simulants. The existing Martian simulants have differences due to varying source materials and design parameters. Additional simulants are needed because the few available simulants do not replicate the compositional diversity of Martian regolith. This study discusses the development of a low-cost construction simulant of Mars. The area of Winder Nai in Pakistan was selected for field sampling of basalt because of local availability and easy access. The dust was produced from rock samples through mechanical crushing and grinding. The physical properties, composition, mineralogy, and surface morphology were evaluated via geotechnical tests, Energy Dispersive X-ray (EDX) spectroscopy, X-ray Diffraction (XRD), and Scanning Electron Microscopy (SEM), respectively. The designed simulant has a well-graded particle size distribution with a particle density and bulk density of 2.58 g/cm3 and 1.16 g/cm3, respectively. The elemental composition of Winder Nai Mars Simulant (WNMS) is within ±5 wt% of the Rocknest and the average Martian regolith composition except for SO3. For SiO2, Al2O3, and Fe2O3, WNMS has a good match with the Martian regolith. The content of CaO and TiO2 in WNMS is higher than, and content of MgO is lower than, the average Martian values. The rock can be classified as basalt based on the Total Alkali Silica (TAS) diagram. XRD spectrum indicates the occurrence of plagioclase and pyroxene as the main signature minerals of basalt. The particle morphology of WNMS is angular to subangular, and the simulant indicates the presence of 3.8 wt% highly paramagnetic particles. The volatile loss is 0.25 wt% at 100 °C, 1.73 wt% at 500 °C, and 3.05 wt% at 950 °C. The composition of WNMS, basaltic mineralogy, morphology, magnetic properties, and volatile content are comparable with MMS-2 and a few other simulants.

Structural Condition Classification of Railway Bridge KW51 Before, During, and After Retrofitting

AbstractA linear classification algorithm for various structural states (before, during, and after retrofitting) of railway steel arch bridge KW51 based on Linear Discriminant Analysis (LDA) of principal components is proposed. The technique is typically employed in other fields, such as genetics, but its use in civil engineering is still limited. The method is applied in two steps, first, the original vibration measurements are projected to a lower dimensional subspace using Principal Component Analysis (PCA). The significant principal components are provided as inputs to LDA to constitute the newly transformed subspace. Joining PCA and LDA improves the performance aptitude of LDA when only first major principal components hold the main signature of the features. The acceleration datasets that represent bridge conditions under train passage on the steel arch railway bridge in Belgium, mentioned as bridge KW51 have been utilized for validation of the algorithm. The outcome of the visualization process is further analyzed using three clustering methods (kmeans, Fuzzy C means, and Gaussian Mixture Modelling). The confusion matrix is used to examine the performance of the clustering methods. The proposed algorithm provides promising results that outperformed other classification methods.

Plasma-Made Nanogold for DNA Sensing with SERS

Facilitated electrochemical properties of plasma are crucial for improving functional nanomaterials synthesis and design for novel sensor development. Controlled customization and functionality tailoring at multiscale is the targeted challenge for better detection devices performance. In the modern era of optoelectronics, among various probing approaches, plasmonic sensing accompanied by Raman, FTIR or Fluorescent spectroscopy is considered a tool for the efficient investigation of molecular properties. In particular, Raman scattering is often called SERS (surface-enhanced Raman scattering) due to plasmonic enhancers, which are used to improve the probing of analytes at a reduced scale. This feature is extremely useful for biologically relevant analytical tasks when samples alike DNA and similar need to be investigated fast and accurately. DNA/RNA-related investigations are highly important in modern nanomedicine due to the solid progress of bionanotechnology, DNA vaccines, and functional gene engineering. DNA is the most valued substance for microbiologists because it contains information about bio-species' nature.[1] Currently, the number of molecular-sensitive methods for DNA-level study is quite limited, among which PCR (polymer chain reaction) related methods dominate the field. However, it is challenging to investigate it with optical techniques like SERS. Despite being promising, SERS is still under technological and analytical improvement. Better performance comes with sophisticated plasmonic nanomaterials, which provide considerably improved photon scattering due to the strongly localized field confinement effect.[2] In the current report, a well-performing nanoplasmonic sensor was designed using a plasma-driven electrochemical reduction mechanism. Exploiting atmospheric pressure He-plasma jet setup operating kHz frequency, the reactive oxidative species donated electrons via liquid-gas electrochemistry towards the Ar-delivered Au(3+)-containing microdroplets. Through this method, microscaled aggregates composed of AuNPs were obtained from the nebulized ionic gold liquid precursor. Due to the strong coupling between nanoparticles, a high analytical enhancement factor of about 107 was achieved and the substrate allowed to obtain Raman fingerprints of bacterial DNA fragments (M. luteus and S. aureus, E. coli, J. lividum) at nanovolume sample quantities. In addition, main DNA molecular vibrational signatures associated with nucleobase motions were extracted from spectra collected and used to classify the bacterial strains reliably by employing statistical principal component analysis.

MDB-19. MULTIOMIC PROFILING OF MEDULLOBLASTOMA REVEALS SUBTYPE-SPECIFIC TARGETABLE ALTERATIONS AT THE PROTEOME AND N-GLYCAN LEVEL

Abstract Medulloblastomas (MBs) are malignant pediatric brain tumors which are clinically and histologically very heterogeneous. Epigenomic and transcriptomic analyses have advanced the understanding of these tumors and four main molecular subgroups – which themselves comprise several subtypes- have been defined: WNT-activated MB, Sonic hedgehog (SHH)-activated MB, Group3 and Group4 MB. Despite tremendous advances in classification and stratification, the pathogenesis of subtypes is still poorly understood and there is still a lack of targeted therapies. In contrast to nucleic acids, proteins more directly account for the phenotype and hold the potential to discover clinically relevant phenotypes, new biomarkers and therapy targets. In this study, we put together a harmonized cohort of 167 MB samples and integrated proteome data with DNA methylome and N-glycan data. At proteome level, we found six stable subtypes which could be assigned to two main molecular signatures namely-transcriptional/translational processes (pWNT, pG3myc and pSHHt) and synaptic/immunological processes (pG3, pG4 and pSHHs). pG3myc MB showed poor survival and accumulated high risk features such as anaplastic histology, epigenetic subtype II and MYC amplification. They showed an overlap of proteome patterns with favorable pWNT MBs but displayed significantly different protein abundancies of the vincristine resistance associated TriC/CCT complex and N-glycan turnover associated factors. Of note. N-glycan profiles distinguished MB subtypes and pG3myc MBs were enriched by complex bisecting N-glycans. We further identified Tenascin C (TNC) and Palmdelphin (PALMD) as suitable biomarkers for the pWNT and pG3myc MBs, respectively. Integration of proteome and DNA methylome data revealed that pWNT MBs showed the highest correlation of data modalities among MB subtypes, indicating a higher conservation of biological processes compared to other proteome subtypes. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.