Modern machine-learning applications in ambient ionization mass spectrometry.

This article provides a comprehensive overview of the applications of methods of machine learning (ML) and artificial intelligence (AI) in ambient ionization mass spectrometry (AIMS). AIMS has emerged as a powerful analytical tool in recent years, allowing for rapid and sensitive analysis of various samples without the need for extensive sample preparation. The integration of ML/AI algorithms with AIMS has further expanded its capabilities, enabling enhanced data analysis. This review discusses ML/AI algorithms applicable to the AIMS data and highlights the key advancements and potential benefits of utilizing ML/AI in the field of mass spectrometry, with a focus on the AIMS community.

Mass spectrometry for neurosurgery: Intraoperative support in decision-making.

Ambient ionization mass spectrometry was proved to be a powerful tool for oncological surgery. Still, it remains a translational technique on the way from laboratory to clinic. Brain surgery is the most sensitive to resection accuracy field since the balance between completeness of resection and minimization of nerve fiber damage determines patient outcome and quality of life. In this review, we summarize efforts made to develop various intraoperative support techniques for oncological neurosurgery and discuss difficulties arising on the way to clinical implementation of mass spectrometry-guided brain surgery.

From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited.

Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.

Ultrafast dynamics of fluorene initiated by highly intense laser fields.

We present an investigation of the ultrafast dynamics of the polycyclic aromatic hydrocarbon fluorene initiated by an intense femtosecond near-infrared laser pulse (810 nm) and probed by a weak visible pulse (405 nm). Using a multichannel detection scheme (mass spectra, electron and ion velocity-map imaging), we provide a full disentanglement of the complex dynamics of the vibronically excited parent molecule, its excited ionic states, and fragments. We observed various channels resulting from the strong-field ionization regime. In particular, we observed the formation of the unstable tetracation of fluorene, above-threshold ionization features in the photoelectron spectra, and evidence of ubiquitous secondary fragmentation. We produced a global fit of all observed time-dependent photoelectron and photoion channels. This global fit includes four parent ions extracted from the mass spectra, 15 kinetic-energy-resolved ionic fragments extracted from ion velocity map imaging, and five photoelectron channels obtained from electron velocity map imaging. The fit allowed for the extraction of 60 lifetimes of various metastable photoinduced intermediates.

On the thermodynamic stability of polycations.

We present a simple approximation to estimate the largest charge that a given molecule can hold until fragmentation into smaller charged species becomes more energetically favorable. This approximation solely relies on the ionization potentials, electron affinities of the parent and fragment species, and also on the neutral parent's dissociation energy. By parameterizing these quantities, it is possible to obtain analytical phase diagrams of polycationic stability. We demonstrate the applicability of this approach by discussing the maximal charge dependence on the size of the molecular system. A numerical demonstration for linear polyenes, monocyclic annulenes, and helium clusters is provided.

Escape from textured adsorbing surfaces.

The escape dynamics of sticky particles from textured surfaces is poorly understood despite importance to various scientific and technological domains. In this work, we address this challenge by investigating the escape time of adsorbates from prevalent surface topographies, including holes/pits, pillars, and grooves. Analytical expressions for the probability density function and the mean of the escape time are derived. A particularly interesting scenario is that of very deep and narrow confining spaces within the surface. In this case, the joint effect of the entrapment and stickiness prolongs the escape time, resulting in an effective desorption rate that is dramatically lower than that of the untextured surface. This rate is shown to abide a universal scaling law, which couples the equilibrium constants of adsorption with the relevant confining length scales. While our results are analytical and exact, we also present an approximation for deep and narrow cavities based on an effective description of one-dimensional diffusion that is punctuated by motionless adsorption events. This simple and physically motivated approximation provides high-accuracy predictions within its range of validity and works relatively well even for cavities of intermediate depth. All theoretical results are corroborated with extensive Monte Carlo simulations.

Macroscopic behavior of populations of quadratic integrate-and-fire neurons subject to non-Gaussian white noise.

We study macroscopic behavior of populations of quadratic integrate-and-fire neurons subject to non-Gaussian noises; we argue that these noises must be α-stable whenever they are delta-correlated (white). For the case of additive-in-voltage noise, we derive the governing equation of the dynamics of the characteristic function of the membrane voltage distribution and construct a linear-in-noise perturbation theory. Specifically for the recurrent network with global synaptic coupling, we theoretically calculate the observables: population-mean membrane voltage and firing rate. The theoretical results are underpinned by the results of numerical simulation for homogeneous and heterogeneous populations. The possibility of the generalization of the pseudocumulant approach to the case of a fractional α is examined for both irrational and fractional rational α. This examination seemingly suggests the pseudocumulant approach or its modifications to be employable only for the integer values of α=1 (Cauchy noise) and 2 (Gaussian noise) within the physically meaningful range (0;2]. Remarkably, the analysis for fractional α indirectly revealed that, for the Gaussian noise, the minimal asymptotically rigorous model reduction must involve three pseudocumulants and the two-pseudocumulant model reduction is an artificial approximation. This explains a surprising gain of accuracy for the three-pseudocumulant models as compared to the two-pseudocumulant ones reported in the literature.

Soil moisture conditions alter behavior of entomopathogenic nematodes.

BACKGROUND: A variety of environmental factors can disrupt biotic interactions between plants, insects and soil microorganisms with consequences for agricultural management and production. Many of these belowground interactions are mediated by volatile organic compounds (VOCs) which can be used for communication under appropriate environmental conditions. Behavioral responses to these compounds may likewise be dependent on varying soil conditions which are influenced by a changing climate. To determine how changing environmental conditions may affect VOC-mediated biotic interactions, we used a belowground system where entomopathogenic nematodes (EPNs) - tiny roundworm parasitoids of soil-borne insects - respond to VOCs by moving through the soil pore matrix. Specifically, we used two genera of EPNs - Heterorhabditis and Steinernema - that are known to respond to four specific terpenes - α-pinene, linalool, d-limonene and pregeijerene - released by the roots of plants in the presence of herbivores. We assessed the response of these nematodes to these terpenes under three moisture regimes to determine whether drier conditions or inundated conditions may influence the response behavior of these nematodes. RESULTS: Our results illustrate that the recovery rate of EPNs is positively associated with soil moisture concentration. As soil moisture concentration increases from 6% to 18%, substantially more nematodes are recovered from bioassays. In addition, we find that soil moisture influences EPN preference for VOCs, as illustrated in the variable response rates. Certain compounds shifted from acting as a repellent to acting as an attractant and vice versa depending on the soil moisture concentration. CONCLUSION: On a broad scale, we demonstrate that soil moisture has a significant effect on EPN host-seeking behavior. EPN efficacy as biological control agents could be affected by climate change projections that predict varying soil moisture concentrations. We recommend that maintaining nematodes as biological control agents is essential for sustainable agriculture development, as they significantly contribute not only to soil health but also to efficient pest management. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Metadynamics simulations with Bohmian-style bias potential.

Here, we present a parametrization of the metadynamics simulations for reactions involving breaking the chemical bonds along a single collective variable coordinate. The parameterization is based on the similarity between the bias potential in metadynamics and the quantum potential in the de Broglie-Bohm formalism. We derive the method and test it on two prototypical reaction types: proton transfer and breaking of the cyclohexene cycle (reversed Diels-Alder reaction).

Altered lipid metabolism in synovial fibroblasts of individuals at risk of developing rheumatoid arthritis.

OBJECTIVE: Fibroblast-like synoviocytes (FLS) can augment the inflammatory process observed in synovium of patients with rheumatoid arthritis (RA). A recent transcriptomic study in synovial biopsies revealed changes in metabolic pathways before disease onset in absence of synovial tissue inflammation. This raises the question whether alterations in cellular metabolism in tissue resident FLS underlie disease pathogenesis. MATERIALS AND METHODS: To study this, we compared the metabolic profile of FLS isolated from synovial biopsies from individuals with arthralgia who were autoantibody positive but without any evidence of arthritis (RA-risk individuals, n = 6) with FLS from patients with RA (n = 6), osteoarthritis (OA, n = 6) and seronegative controls (n = 6). After synovial digestion, FLS were cultured in vitro and cellular metabolism was assessed using quantitative PCR, flow cytometry, XFe96 Seahorse Analyzer and tritium-labelled oleate oxidation assays. RESULTS: Real-time metabolic profiling revealed that basal (p < 0.0001) and maximum mitochondrial respiration (p = 0.0024) were significantly lower in RA FLS compared with control FLS. In all donors, basal respiration was largely dependent on fatty acid oxidation while glucose was only highly used by FLS from RA patients. Moreover, we showed that RA-risk and RA FLS are less metabolically flexible. Strikingly, mitochondrial fatty acid ß-oxidation was significantly impaired in RA-risk (p = 0.001) and RA FLS (p < 0.0001) compared with control FLS. CONCLUSION: Overall, this study showed several metabolic alterations in FLS even in absence of synovial inflammation, suggesting that these alterations already start before clinical manifestation of disease and may drive disease pathogenesis.

Reviving the anatomic past: Breathing new life into historic anatomical teaching tools.

The last two decades have seen a shift in the way anatomy education is delivered. With the introduction of blended learning, cadaveric dissection is no longer the be all and end all and, in many cases, the continuing role of anatomical teaching artefacts has declined after decades of prominence. While some institutions have abandoned their archaic anatomical collections and medical museums completely, others have invested in their technological enhancement. We describe the integration of historical teaching artefacts into contemporary anatomy education through the development of an interactive online e-platform and shed light on the enduring pedagogic value of past anatomical teaching specimen.

TDP-43 Pathology Exacerbates Cognitive Decline in Primary Age-Related Tauopathy.

OBJECTIVE: Primary age-related tauopathy (PART) refers to tau neurofibrillary tangles restricted largely to the medial temporal lobe in the absence of significant beta-amyloid plaques. PART has been associated with cognitive impairment, but contributions from concomitant limbic age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) are underappreciated. METHODS: We compare prevalence of LATE-NC and vascular copathologies in age- and Braak-matched patients with PART (n = 45, Braak stage I-IV, Thal phase 0-2) or early stage Alzheimer disease neuropathologic change (ADNC; n = 51, Braak I-IV, Thal 3-5), and examine their influence on clinical and cognitive decline. RESULTS: Concomitant LATE-NC and vascular pathology were equally common, and cognition was equally impaired, in PART (Mini-Mental State Examination [MMSE] = 24.8 ± 6.9) and ADNC (MMSE = 24.2 ± 6.0). Patients with LATE-NC were more impaired than those without LATE-NC on the MMSE (by 5.8 points, 95% confidence interval [CI] = 3.0-8.6), Mattis Dementia Rating Scale (DRS; 17.5 points, 95% CI = 7.1-27.9), Clinical Dementia Rating, sum of boxes scale (CDR-sob; 5.2 points, 95% CI = 2.1-8.2), memory composite (0.8 standard deviations [SD], 95% CI = 0.1-1.6), and language composite (1.1 SD, 95% CI = 0.2-2.0), and more likely to receive a dementia diagnosis (odds ratio = 4.8, 95% CI = 1.5-18.0). Those with vascular pathology performed worse than those without on the DRS (by 10.2 points, 95% CI = 0.1-20.3) and executive composite (1.3 SD, 95% CI = 0.3-2.3). Cognition declined similarly in PART and ADNC over the 5 years preceding death; however, LATE-NC was associated with more rapid decline on the MMSE (ß = 1.9, 95% CI = 0.9-3.0), DRS (ß = 7.8, 95% CI = 3.4-12.7), CDR-sob (ß = 1.9, 95% CI = 0.4-3.7), language composite (ß = 0.5 SD, 95% CI = 0.1-0.8), and vascular pathology with more rapid decline on the DRS (ß = 5.2, 95% CI = 0.6-10.2). INTERPRETATION: LATE-NC, and to a lesser extent vascular copathology, exacerbate cognitive impairment and decline in PART and early stage ADNC. ANN NEUROL 2022;92:425-438.

α-Synuclein Seed Amplification in CSF and Brain from Patients with Different Brain Distributions of Pathological α-Synuclein in the Context of Co-Pathology and Non-LBD Diagnoses.

OBJECTIVE: The purpose of this study was to determine the sensitivity and specificity of α-synuclein seed amplification assay (αSyn-SAA) in antemortem and postmortem cerebrospinal fluid (CSF) of autopsy-confirmed patients with different distributions of pathological αSyn, co-pathologies, and clinical diagnoses. METHODS: The αSyn-SAA was used to test antemortem CSF samples from 119 subjects with a variety of clinical syndromes and standardized neuropathological examinations from Oregon Health and Science University (OHSU) and University of California San Diego (UCSD; 56 additional postmortem CSF samples available). The αSyn-SAA was also applied to frontal cortex and amygdala homogenates. Sensitivity and specificity were compared across distributions of αSyn pathology. Clinical data and co-pathologies were compared across αSyn-SAA positive and negative groups. RESULTS: Fifty-three individuals without and 66 with αSyn-pathology (neocortical [n = 38], limbic [n = 7], and amygdala-predominant [n = 21]) were included. There was a sensitivity of 97.8% and specificity of 98.1% of the αSyn-SAA to identify patients with limbic/neocortical pathology from antemortem CSF. Sensitivity to detect amygdala-predominant pathology was only 14.3%. Postmortem CSF and brain tissue αSyn-SAA analyses also showed higher assay positivity in samples from limbic/neocortical cases. INTERPRETATION: CSF αSyn-SAA reliably identifies αSyn seeds in patients with diffuse αSyn pathology in the context of co-pathology and non-Lewy body disease (LBD) diagnoses. The analysis of brain homogenates suggests that pathological αSyn in the amygdala might differ from pathological αSyn in the frontal cortex. The αSyn-SAA might facilitate the differential diagnosis of dementias with mixed pathologies. ANN NEUROL 2022;92:650-662.

Raman dissipative soliton source of ultrashort pulses in NIR-III spectral window.

We present a novel fiber source of ultrashort pulses at the wavelength of 1660 nm based on the technique of external cavity Raman dissipative soliton generation. The output energy of the generated 30 ps chirped pulses is in the range of 0.5-3.6 nJ with a slope efficiency of 57%. Numerical simulations are in excellent agreement with the experimental results and the shape of the compressed pulses. The compressed pulses consist of a central part with a duration of 300 fs and a weak pedestal. Our results clearly demonstrate the potential to extend the spectral range of the Raman-assisted technique for generating ultra-short pulses to new frequency regions, including biomedical windows. This paves the way for the development of new dissipative soliton sources in these bands.

All-fiber amplification of highly chirped dissipative solitons around a 1.3 micron using stimulated Raman scattering.

An all-fiber amplification of highly chirped dissipative solitons (DSs) by stimulated Raman scattering in a standard passive fiber with continuous-wave pumping is demonstrated for the first time to our knowledge. DSs with a duration of 20 ps and a repetition rate of 15.6 MHz at a wavelength of 1275 nm are amplified by a pump wave at 1205 nm. On-off Raman gain dependence on the amplifier length and pump power, as well as the pumping configuration, are experimentally studied. Uniform amplification has been achieved with a net gain of 10 dB resulting in a pulse energy of 13 nJ at backward pumping. Further Raman amplification is limited by emerging the next Stokes component. The output pulses are compressed by a factor of 50 down to a duration of 400 fs. As a result, the peak power reached the level of 9 kW. The demonstrated scheme can be a simple and robust alternative to the widely used parametric amplification of chirped pulses outside the dopant amplification band, and the resulting pulses can be used in multiphoton microscopy and other applications.

Modal phase-locking in multimode nonlinear optical fibers.

Spatial beam self-cleaning, a manifestation of the Kerr effect in graded-index multimode fibers, involves a nonlinear transfer of power among modes, which leads to robust bell-shaped output beams. The resulting mode power distribution can be described by statistical mechanics arguments. Although the spatial coherence of the output beam was experimentally demonstrated, there is no direct study of modal phase evolutions. Based on a holographic mode decomposition method, we reveal that nonlinear spatial phase-locking occurs between the fundamental and its neighboring low-order modes, in agreement with theoretical predictions. As such, our results dispel the current belief that the spatial beam self-cleaning effect is the mere result of a wave thermalization process.

High Reactivity of Supermolecular Nanoentities of a Vitamin B12 Derivative in Langmuir-Schaefer Films Toward Gaseous Toxins.

Recently, we have described the first supermolecular nanoentities (SMEs) of a vitamin B12 derivative, viz., a monocyano form of heptabutyl cobyrinate ((CN-)BuCby), unique nanoparticles with strong noncovalent intermolecular interactions, and emerging optical and redox properties. In this work, the fast response of thin films based on the SMEs of the B12 derivative to gaseous toxins (viz., hydrogen cyanide, ammonia, sulfur dioxide, and hydrogen sulfide) particularly dangerous for humans was demonstrated. The reaction between SMEs of (CN-)BuCby in Langmuir-Schaefer (LS) films and HCN generates dicyano species and proceeds ca. 5-fold more rapidly than the process involving drop-coated films that contain (CN-)BuCby in molecular form. The highest sensitivity toward HCN was achieved by using thicker LS films. The reaction proceeds reversibly: upon exposure to air, the dicyano complex undergoes partial decyanation. The decyanated complex retains reactivity toward HCN for at least four subsequent cycles. The processes involving SMEs of (CN-)BuCby and NH3, SO2, and H2S are irreversible, and the sensitivity of the films toward these gases is lower in comparison with HCN. Presented data provides mechanistic information on the reactions involving solid vitamin B12 derivatives and gaseous toxins. In the case of NH3, deprotonation of the coordinated Co(III)-ion water molecule occurs, and the generated hydroxocyano species exhibit high air stability. After binding of SO2, a mixture of sulfito and dicyano species is produced, and the regenerated film contains aquacyano and diaqua or aquahydroxo species, which possess high reactivity toward gaseous toxins. Reaction with H2S produces a mixture of the Co(III)-dicyano form and Co(II)-species containing sulfide oxidation products, which are resistant to aerobic oxidation. Our findings can be used for the development of naked-eye, electronic optic, and chemiresistive sensors toward gaseous toxins with improved reactivity for prompt cyanide detection in air, blood, and plant samples and for analysis of exhaled gases for the diagnosis of diseases.

Supermolecular Nanoentities of Vitamin B12 Derivative as a Link in the Evolution of the Parent Molecules During Self-Assembly at the Air-Water Interface.

Nanoarchitectures with promising properties have now been formed from many important biomolecules. However, the preparation of nanoparticles of vitamin B12 and its derivatives remains an ongoing research challenge. This paper describes the formation of supermolecular nanoentities (SMEs) of vitamin B12 derivatives, unique nanoparticles with strong noncovalent intermolecular interactions, emerging properties, and activity. These were created by a nanoarchitectonic approach using directed assembly of layers at the air-water interface as a link in the chain of evolution of the parent molecules under specially created conditions. Such layers can be represented as a nanocosm, where, at a critical density, the assemblies act as nanoreactors in which the transformation of the original material occurs. The discovered SMEs not only replicate the functioning of vitamin B12 assemblies with proteins in living organisms and act as vitamin B12-depended enzymes but also demonstrate important advantages over vitamin B12. They are more efficient in oxygen reduction/evolution reactions and in transformation into other forms. These SMEs, in performing advanced tasks, are an alternative to widely used materials based on noble metals for catalysis, medicine, and environment protection. Our findings open new perspectives both for the fabrication of novel SMEs of biomolecules and for a better understanding of the evolution of biomolecules in nature.

Stochastic parametric excitation of convective heat transfer.

We study the parametric excitation of the free thermal convection in a horizontal layer and a rectangular cell by random vertical vibrations. The mathematical formulation we use allows one to explore the cases of heating from below and above and the low-gravity conditions. The excitation threshold of the second moments of the current velocity and the temperature perturbations are derived. The heat flux through the system quantified by the Nusselt number is reported to be related to the second moment of temperature perturbations; therefore, the threshold of the stochastic excitation of second moments gives the threshold for the excitation of the convective heat transfer. Comparison of the stochastic parametric excitation with the effect of high-frequency periodic modulation reveals dramatic dissimilarity between the two. This article is part of the theme issue 'New trends in pattern formation and nonlinear dynamics of extended systems'.

Describing nuclear quantum effects in vibrational properties using molecular dynamics with Wigner sampling.

In this work we discuss the generally applicable Wigner sampling and introduce a new, simplified Wigner sampling method, for computationally effective modeling of molecular properties containing nuclear quantum effects and vibrational anharmonicity. For various molecular systems test calculations of (a) vibrationally averaged rotational constants, (b) vibrational IR spectra and (c) photoelectron spectra have been performed. The performance of Wigner sampling has been assessed by comparing with experimental data and with results of other theoretical models, including harmonic and VPT2 approximations. The developed simplified Wigner sampling method shows advantages in application to large and flexible molecules.