bluuebunny/crossref_metadata_2025_split huggingface dataset:
EMBL-MCF 2.0: an LC-MS/MS method and corresponding library for high-confidence targeted and untargeted metabolomics using low-adsorption HILIC chromatography
Authors: Dekina Svitlana , Alexandrov Theodore , Drotleff Bernhard 
Published: October 2024

Abstract
Introduction
Over the past two decades, liquid chromatography-mass spectrometry (LC-MS)-based metabolomics has experienced significant growth, playing a crucial role in various scientific disciplines. However, despite these advance-ments, metabolite identification (MetID) remains a significant challenge. To address this, stringent MetID requirements were established, emphasizing the necessity of aligning experimental data with authentic reference standards using multiple criteria. Establishing dependable methods and corresponding libraries is crucial for instilling confidence in MetID and driving further progress in metabolomics.

Objective
The EMBL-MCF 2.0 LC-MS/MS method and public library was designed to facilitate both targeted and untargeted metabolomics with exclusive focus on endogenous, polar metabolites, which are known to be challenging to analyze due to their hydrophilic nature. By accompanying spectral data with robust retention times obtained from authentic standards and low-adsorption chromatography, high confidence MetID is achieved and accessible to the metabolomics community.

Methods
The library is built on hydrophilic interaction liquid chromatography (HILIC) and state-of-the-art low adsorption LC hardware. Both high-resolution tandem mass spectra and manually optimized multiple reaction monitoring (MRM) transitions were acquired on an Orbitrap Exploris 240 and a QTRAP 6500+, respectively.

Results
Implementation of biocompatible HILIC has facilitated the separation of isomeric metabolites with significant enhancements in both selectivity and sensitivity. The resulting library comprises a diverse collection of more than 250 biologically relevant metabolites. The methodology was successfully applied to investigate a variety of biological matrices, with exemplary findings showcased using murine plasma samples.

Conclusions
Our work has resulted in the development of the EMBL-MCF 2.0 library, a powerful resource for sensitive metabolomics analyses and high-confidence MetID. The library is freely accessible and available in the universal .msp file format under the CC-BY 4.0 license: mona.fiehnlab.ucdavis.edu https://mona.fiehnlab.ucdavis.edu/spectra/browse?query=exists(tags.text:%27EMBL-MCF_2.0_HRMS_Library%27), EMBL-MCF 2.0 HRMS https://www.embl.org/groups/metabolomics/instrumentation-and-software/#MCF-library.
Dopaminergic neuron metabolism: relevance for understanding Parkinson’s disease
Authors: Flores-Ponce Xóchitl , Velasco Iván 
Published: October 2024

Abstract
Background
Dopaminergic neurons from the substantia nigra pars compacta (SNc) have a higher susceptibility to aging-related degeneration, compared to midbrain dopaminergic cells present in the ventral tegmental area (VTA); the death of dopamine neurons in the SNc results in Parkinson´s disease (PD). In addition to increased loss by aging, dopaminergic neurons from the SNc are more prone to cell death when exposed to genetic or environmental factors, that either interfere with mitochondrial function, or cause an increase of oxidative stress. The oxidation of dopamine is a contributing source of reactive oxygen species (ROS), but this production is not enough to explain the differences in susceptibility to degeneration between SNc and VTA neurons.

Aim of review
In this review we aim to highlight the intrinsic differences between SNc and VTA dopamine neurons, in terms of gene expression, calcium oscillations, bioenergetics, and ROS responses. Also, to describe the changes in the pentose phosphate pathway and the induction of apoptosis in SNc neurons during aging, as related to the development of PD.

Key scientific concepts of review
Recent work showed that neurons from the SNc possess intrinsic characteristics that result in metabolic differences, related to their intricate morphology, that render them more susceptible to degeneration. In particular, these neurons have an elevated basal energy metabolism, that is required to fulfill the demands of the constant firing of action potentials, but at the same time, is associated to higher ROS production, compared to VTA cells. Finally, we discuss how mutations related to PD affect metabolic pathways, and the related mechanisms, as revealed by metabolomics.
Assessment of Gastric Remnant Activity, Symptoms, and Quality of Life Following Gastric Bypass
Authors: Wang Tim Hsu-Han , Varghese Chris , Calder Stefan , Gharibans Armen A. , Evennett Nicholas , Beban Grant , Schamberg Gabriel , O’Grady Greg 
Published: October 2024

Abstract
Introduction
While most gastric bypass patients recover well, some experience long-term complications, including nausea, abdominal pain, food intolerance, and dumping. This study aimed to evaluate symptoms and quality of life (QoL) in association with the residual activity of the remnant stomach.

Methods
Patients undergoing gastric bypass and conversion-to-bypass were recruited. The Gastric Alimetry® System (Auckland, NZ) was employed, comprising a high-resolution electrode array, wearable reader, and validated symptom logging app. The protocol comprised 30-min fasting baseline, a 218-kCal meal stimulus, and 4-h of post-prandial recordings. Symptoms and QoL were evaluated using validated questionnaires. Remnant gastric electrophysiology evaluation included frequency, BMI-adjusted amplitude, and Gastric Alimetry Rhythm Index (GA-RI, reflecting pacemaker stability), with comparison to validated reference intervals and matched controls.

Results
Thirty-eight participants were recruited with mean time from bypass 46.8 ± 28.6 months. One-third of patients showed moderate to severe post-prandial symptoms, with patients’ median PAGI-SYM 28 ± 19 vs controls 9 ± 17 (p < 0.01); PAGI-QOL 37 ± 31 vs 135 ± 22 (p < 0.0001). Remnant gastric function was markedly degraded shown by undetectable frequencies in 84% (vs 0% in controls) and low GA-RI (0.18 ± 0.08 vs 0.51 ± 0.22 in controls; p < 0.0001; reference range > 0.25). Impaired GA-RI and amplitude were correlated with worse PAGI-SYM and PAGI-QOL scores.

Conclusion
One-third of post-bypass patients suffered significant upper GI symptoms with reduced QoL. The bypassed remnant stomach shows highly deranged electrophysiology in-situ, reflecting disuse degeneration. These derangements correlated with QoL; however, causality is not implied by the present study.
Holistic Sensitivity Analysis for Long-Term Energy Demand Prediction of Battery Electric Vehicles
Authors: Schäfers Lukas , Iravanimanesh Sahba , Franke Kai , Savelsberg Rene , Pischinger Stefan 
Published: October 2024

AbstractAccurate and robust range estimation algorithms for battery electric vehicles have the potential to reduce range anxiety, increase the acceptance of lower-range vehicles, and improve the overall driving experience. However, developing such algorithms faces challenges due to the complexity of the driver-vehicle-environment system and the multitude of factors influencing a vehicle's energy demand. To address these challenges, this paper introduces a sensitivity analysis focused on driver- and environment-related factors, which are notably difficult to predict. Employing a global sensitivity analysis for factor prioritization, this study delineates and assesses the parameters and their value distributions using a validated vehicle simulation model. The co-simulation of a powertrain and an auxiliaries model enables the parameter-specific investigation of parameters related to the thermal system. The results are scenario-individual parameter rankings that show the importance of the considered factors in prediction algorithms and guide the strategy for the development of these algorithms. The acceleration behavior of the driver, often emphasized in literature, is shown to be of secondary importance to energy consumption. Moreover, factors such as air density and wind speed are identified as crucial in highway driving scenarios, whereas outside temperature and the probability of stopping at traffic lights are critical in urban settings. For validation purposes, the resulting rankings of the sensitivity study are validated by means of a convergence analysis.
The uniqueness of unconditional basis of the 2-convexified Tsirelson space, revisited
Authors: Albiac Fernando , Ansorena José L. 
Published: October 2024

AbstractOne of the hallmarks in the study of the classification of Banach spaces with a unique (normalized) unconditional basis was the unexpected result by Bourgain, Casazza, Lindenstrauss, and Tzafriri from their 1985 Memoir that the 2-convexified Tsirelson space $${\mathcal {T}}^{(2)}$$

T

(
2
)

had that property (up to equivalence and permutation). Indeed, on one hand, finding a “pathological” space (i.e., not built out as a direct sum of the only three classical sequence spaces with a unique unconditional basis) shattered the hopeful optimism of attaining a satisfactory description of all Banach spaces which enjoy that important structural feature. On the other hand it encouraged furthering a research topic that had received relatively little attention until then. After forty years, the advances on the subject have shed light onto the underlying patterns shared by those spaces with a unique unconditional bases belonging to the same class, which has led to reproving the original theorems with fewer technicalities. Our motivation in this note is to revisit the aforementioned result on the uniqueness of unconditional basis of $${\mathcal {T}}^{(2)}$$

T

(
2
)

from the current state-of-art of the subject and to fill in some details that we missed from the original proof.
Rapid Geomagnetic Variations During High‐Speed Stream, Sheath and Magnetic Cloud‐Driven Geomagnetic Storms From 1996 to 2023
Authors: Pedersen M. N. , Juusola L. , Vanhamäki H. , Aikio A. T. , Viljanen A. 
Published: October 2024

AbstractThe most detrimental geomagnetically induced currents (GICs) documented to date have all taken place during geomagnetic storms. Yet, the probability of GICs throughout geomagnetic storms driven by different solar wind transients, such as high‐speed streams/stream interaction regions (HSS/SIR) or interplanetary coronal mass ejection (ICME) sheaths and magnetic clouds (MC), is poorly understood. We present an algorithm to detect geomagnetic storms and storm phases, resulting in a catalog of 755 geomagnetic storms from January 1996 to June 2023 with the solar wind drivers. Using these storms and the IMAGE magnetometer network, we study the temporal and spatial evolution of spikes in the time derivative of the horizontal component of the external magnetic field, , greater than 0.5 nT/s during geomagnetic storms driven by HSS/SIR, sheaths and MCs. Spikes occur more often toward the end of the storm main phase for HSS/SIR and MC‐driven storms, while sheaths have spikes throughout the entire main phase. During the main phase most spikes occur in the morning sector around 05 magnetic local time (MLT) and the extent in MLT is narrowest for MCs and widest for sheaths. However, spikes in the pre‐midnight sector during the main and recovery phases are most prominent for HSS/SIR‐driven storms. During the storm sudden commencement (SSC), three MLT hotspots exist, the post‐midnight at 04 MLT, pre‐noon at 09 MLT and afternoon at 15 MLT. The pre‐noon hotspot has the highest probability of spikes and the widest extent in magnetic latitude.
Polyploidy mitigates the impact of DNA damage while simultaneously bearing its burden
Authors: Hayashi Kazuki , Horisaka Kisara , Harada Yoshiyuki , Ogawa Yuta , Yamashita Takako , Kitano Taku , Wakita Masahiro , Fukusumi Takahito , Inohara Hidenori , Hara Eiji , Matsumoto Tomonori 
Published: October 2024

AbstractPolyploidy is frequently enhanced under pathological conditions, such as tissue injury and cancer in humans. Polyploidization is critically involved in cancer evolution, including cancer initiation and the acquisition of drug resistance. However, the effect of polyploidy on cell fate remains unclear. In this study, we explored the effects of polyploidization on cellular responses to DNA damage and cell cycle progression. Through various comparisons based on ploidy stratifications of cultured cells, we found that polyploidization and the accumulation of genomic DNA damage mutually induce each other, resulting in polyploid cells consistently containing more genomic DNA damage than diploid cells under both physiological and stress conditions. Notably, despite substantial DNA damage, polyploid cells demonstrated a higher tolerance to its impact, exhibiting delayed cell cycle arrest and reduced secretion of inflammatory cytokines associated with DNA damage-induced senescence. Consistently, in mice with ploidy tracing, hepatocytes with high ploidy appeared to potentially persist in the damaged liver, while being susceptible to DNA damage. Polyploidy acts as a reservoir of genomic damage by mitigating the impact of DNA damage, while simultaneously enhancing its accumulation.
Too big to purge: persistence of deleterious Mutations in Island populations of the European Barn Owl (Tyto alba)
Authors: Lavanchy Eléonore , Cumer Tristan , Topaloudis Alexandros , Ducrest Anne-Lyse , Simon Céline , Roulin Alexandre , Goudet Jérôme 
Published: October 2024

AbstractA key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this study, we used samples from 502 barn owls from continental and island populations across Europe, with the aim of quantifying and comparing the level of inbreeding between populations with differing demographic histories. In addition to comparing inbreeding status, we determined whether inbreeding is due to non-random mating or high co-ancestry within the population. We show that islands have higher levels of inbreeding than continental populations, and that this is mainly due to small effective population sizes rather than recent consanguineous mating. We assess the probability that a region is autozygous along the genome and show that this probability decreased as the number of genes present in that region increased. Finally, we looked for evidence of reduced selection efficiency and purging in island populations. Among island populations, we found an increase in numbers of both neutral and deleterious minor alleles, possibly as a result of drift and decreased selection efficiency but we found no evidence of purging.
UV photochemistry of the L-cystine disulfide bridge in aqueous solution investigated by femtosecond X-ray absorption spectroscopy
Authors: Ochmann Miguel , Harich Jessica , Ma Rory , Freibert Antonia , Kim Yujin , Gopannagari Madhusudana , Hong Da Hye , Nam Daewoong , Kim Sangsoo , Kim Minseok , Eom Intae , Lee Jae Hyuk , Yorke Briony A. , Kim Tae Kyu , Huse Nils 
Published: October 2024

AbstractThe photolysis of disulfide bonds is implicated in denaturation of proteins exposed to ultraviolet light. Despite this biological relevance in stabilizing the structure of many proteins, the mechanisms of disulfide photolysis are still contested after decades of research. Herein, we report new insight into the photochemistry of L-cystine in aqueous solution by femtosecond X-ray absorption spectroscopy at the sulfur K-edge. We observe homolytic bond cleavage upon ultraviolet irradiation and the formation of thiyl radicals as the single primary photoproduct. Ultrafast thiyl decay due to geminate recombination proceeds at a quantum yield of >80 % within 20 ps. These dynamics coincide with the emergence of a secondary product, attributed to the generation of perthiyl radicals. From these findings, we suggest a mechanism of perthiyl radical generation from a vibrationally excited parent molecule that asymmetrically fragments along a carbon-sulfur bond. Our results point toward a dynamic photostability of the disulfide bridge in condensed-phase.
Unsupervised deep denoising for four-dimensional scanning transmission electron microscopy
Authors: Sadri Alireza , Petersen Timothy C. , Terzoudis-Lumsden Emmanuel W. C. , Esser Bryan D. , Etheridge Joanne , Findlay Scott D. 
Published: October 2024

AbstractBy simultaneously achieving high spatial and angular sampling resolution, four dimensional scanning transmission electron microscopy (4D STEM) is enabling analysis techniques that provide great insight into the atomic structure of materials. Applying these techniques to scientifically and technologically significant beam-sensitive materials remains challenging because the low doses needed to minimise beam damage lead to noisy data. We demonstrate an unsupervised deep learning model that leverages the continuity and coupling between the probe position and the electron scattering distribution to denoise 4D STEM data. By restricting the network complexity it can learn the geometric flow present but not the noise. Through experimental and simulated case studies, we demonstrate that denoising as a preprocessing step enables 4D STEM analysis techniques to succeed at lower doses, broadening the range of materials that can be studied using these powerful structure characterization techniques.
Why scanning tunneling spectroscopy of Sr2RuO4 sometimes doesn’t see the superconducting gap
Authors: Valadkhani Adrian , Profe Jonas B. , Kreisel Andreas , Hirschfeld P. J. , Valentí Roser 
Published: October 2024

AbstractScanning tunneling spectroscopy (STS) and scanning tunneling microscopy (STM) are perhaps the most promising ways to detect the superconducting gap size and structure in the canonical unconventional superconductor Sr2RuO4 directly. However, in many cases, researchers have reported being unable to detect the gap at all in STM conductance measurements. Recently, an investigation of this issue on various local topographic structures on a Sr-terminated surface found that superconducting spectra appeared only in the region of small nanoscale canyons, corresponding to the removal of one RuO surface layer. Here, we analyze the electronic structure of various possible surface structures using first principles methods, and argue that bulk conditions favorable for superconductivity can be achieved when removal of the RuO layer suppresses the RuO4 octahedral rotation locally. We further propose alternative terminations to the most frequently reported Sr termination where superconductivity surfaces should be observed.
Aerosol immunization with influenza matrix, nucleoprotein, or both prevents lung disease in pig
Authors: Vatzia Eleni , Paudyal Basudev , Dema Barbara , Carr Brigid Veronica , Sedaghat-Rostami Ehsan , Gubbins Simon , Sharma Bhawna , Moorhouse Elliot , Morris Susan , Ulaszewska Marta , MacLoughlin Ronan , Salguero Francisco J. , Gilbert Sarah C. , Tchilian Elma 
Published: October 2024

AbstractCurrent influenza vaccines are strain-specific and require frequent updates to combat new strains, making a broadly protective influenza vaccine (BPIV) highly desirable. A promising strategy is to induce T-cell responses against internal proteins conserved across influenza strains. In this study, pH1N1 pre-exposed pigs were immunized by aerosol using viral vectored vaccines (ChAdOx2 and MVA) expressing matrix (M1) and nucleoprotein (NP). Following H3N2 challenge, all immunizations (M1, NP or NPM1) reduced lung pathology, but M1 alone offered the greatest protection. NP or NPM1 immunization induced both T-cell and antibody responses. M1 immunization generated no detectable antibodies but elicited M1-specific T-cell responses, suggesting T cell-mediated protection. Additionally, a single aerosol immunization with the ChAdOx vaccine encoding M1, NP and neuraminidase reduced lung pathology. These findings provide insights into BPIV development using a relevant large natural host, the pig.
Sustainable detergent-disinfectant agent based on whey mineralizate and silver nanoparticles for cleaner production in dairy industry
Authors: Blinov Andrey , Blinova Anastasiya , Nagdalian Andrey , Siddiqui Shahida Anusha , Gvozdenko Alexey , Golik Alexey , Rekhman Zafar , Filippov Dionis , Shariati Mohammad Ali , AL-Farga Ammar , Al-maaqar Saleh M. 
Published: October 2024

AbstractDetergents and disinfectants for dairy industry must meet a variety of characteristics, including low toxicity, high antibacterial activity, and excellent rinsing of pollutants from working surfaces. This work presents an innovative detergent-disinfectant agent based on whey mineralizate and silver nanoparticles (Ag NPs), which allows reducing production costs and ensuring high cleanliness of treated surfaces compared to analogues. For this purpose, a method for obtaining sols of Ag NPs stabilized with didecyldimethylammonium bromide (Ag NPs-DDAB) was developed and optimized using neural network algorithms. Characterization of Ag NPs-DDAB showed particles with a radius of 4.5 nm and 20 nm, stable in the pH range from 2 to 11. An acute toxicity study of Ag NPs in mice showed LD50 = 4230 μg/kg. Based on the degree of accumulation and inhalation toxicity, Ag NPs-DDAB are classified as low-hazard chemicals. The developed detergent-disinfectant had a washability of about 90%, high antimicrobial activity (0.005 mg/mL) against Penicillium roqueforti and a sanitary and hygienic effect on coliforms, general contamination and pathogenic microorganisms, a low-corrosive effect and low toxicity (315 mg/mL) to Danio rerio. It was concluded that the use of detergent-disinfectant agent will completely eliminate the consumption of water for the equipment cleaning process and can be used to clean an electrodialysis unit’s circuits, enabling the utilization of secondary waste from membrane milk processing and promoting resource efficiency and cleaner production in the dairy industry.