bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut microbiota and fermentation-derived branched chain hydroxy acids mediate health benefits of yogurt consumption in obese mice
Authors: Daniel Noëmie , Nachbar Renato Tadeu , Tran Thi Thu Trang , Ouellette Adia , Varin Thibault Vincent , Cotillard Aurélie , Quinquis Laurent , Gagné Andréanne , St-Pierre Philippe , Trottier Jocelyn , Marcotte Bruno , Poirel Marion , Saccareau Mathilde , Dubois Marie-Julie , Joubert Philippe , Barbier Olivier , Koutnikova Hana , Marette André 
Published: March 2022

AbstractMeta-analyses suggest that yogurt consumption reduces type 2 diabetes incidence in humans, but the molecular basis of these observations remains unknown. Here we show that dietary yogurt intake preserves whole-body glucose homeostasis and prevents hepatic insulin resistance and liver steatosis in a dietary mouse model of obesity-linked type 2 diabetes. Fecal microbiota transplantation studies reveal that these effects are partly linked to the gut microbiota. We further show that yogurt intake impacts the hepatic metabolome, notably maintaining the levels of branched chain hydroxy acids (BCHA) which correlate with improved metabolic parameters. These metabolites are generated upon milk fermentation and concentrated in yogurt. Remarkably, diet-induced obesity reduces plasma and tissue BCHA levels, and this is partly prevented by dietary yogurt intake. We further show that BCHA improve insulin action on glucose metabolism in liver and muscle cells, identifying BCHA as cell-autonomous metabolic regulators and potential mediators of yogurt’s health effects.
DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics
Authors: Alka Oliver , Shanthamoorthy Premy , Witting Michael , Kleigrewe Karin , Kohlbacher Oliver , Röst Hannes L. 
Published: March 2022

AbstractThe extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges of data-independent acquisition results and their filtering. Another factor is that the creation of assay libraries for data-independent acquisition analysis and the processing of extracted ion chromatograms have not been automated in metabolomics. Here we present a fully automated open-source workflow for high-throughput metabolomics that combines data-dependent and data-independent acquisition for library generation, analysis, and statistical validation, with rigorous control of the false-discovery rate while matching manual analysis regarding quantification accuracy. Using an experimentally specific data-dependent acquisition library based on reference substances allows for accurate identification of compounds and markers from data-independent acquisition data in low concentrations, facilitating biomarker quantification.
Wildfires enhance phytoplankton production in tropical oceans
Authors: Liu Dongyan , Zhou Chongran , Keesing John K. , Serrano Oscar , Werner Axel , Fang Yin , Chen Yingjun , Masque Pere , Kinloch Janine , Sadekov Aleksey , Du Yan 
Published: March 2022

AbstractWildfire magnitude and frequency have greatly escalated on a global scale. Wildfire products rich in biogenic elements can enter the ocean through atmospheric and river inputs, but their contribution to marine phytoplankton production is poorly understood. Here, using geochemical paleo-reconstructions, a century-long relationship between wildfire magnitude and marine phytoplankton production is established in a fire-prone region of Kimberley coast, Australia. A positive correlation is identified between wildfire and phytoplankton production on a decadal scale. The importance of wildfire on marine phytoplankton production is statistically higher than that of tropical cyclones and rainfall, when strong El Niño Southern Oscillation coincides with the positive phase of Indian Ocean Dipole. Interdecadal chlorophyll-a variation along the Kimberley coast validates the spatial connection of this phenomenon. Findings from this study suggest that the role of additional nutrients from wildfires has to be considered when projecting impacts of global warming on marine phytoplankton production.
λ/30 inorganic features achieved by multi-photon 3D lithography
Authors: Jin Feng , Liu Jie , Zhao Yuan-Yuan , Dong Xian-Zi , Zheng Mei-Ling , Duan Xuan-Ming 
Published: March 2022

AbstractIt’s critically important to construct arbitrary inorganic features with high resolution. As an inorganic photoresist, hydrogen silsesquioxane (HSQ) has been patterned by irradiation sources with short wavelength, such as EUV and electron beam. However, the fabrication of three- dimensional nanoscale HSQ features utilizing infrared light sources is still challenging. Here, we demonstrate femtosecond laser direct writing (FsLDW) of HSQ through multi-photon absorption process. 26 nm feature size is achieved by using 780 nm fs laser, indicating super-diffraction limit photolithography of λ/30 for HSQ. HSQ microstructures by FsLDW possess nanoscale resolution, smooth surface, and thermal stability up to 600 °C. Furthermore, we perform FsLDW of HSQ to construct structural colour and Fresnel lens with desirable optical properties, thermal and chemical resistance. This study demonstrates that inorganic features can be flexibly achieved by FsLDW of HSQ, which would be prospective for fabricating micro-nano devices requiring nanoscale resolution, thermal and chemical resistance.
Neuroprotective effects of violacein in a model of inherited amyotrophic lateral sclerosis
Authors: Olivera-Bravo Silvia , Bolatto Carmen , Otero Damianovich Gabriel , Stancov Matías , Cerri Sofía , Rodríguez Paola , Boragno Daniela , Hernández Mir Karina , Cuitiño María Noel , Larrambembere Fernanda , Isasi Eugenia , Alem Diego , Canclini Lucía , Marco Marta , Davyt Danilo , Díaz-Amarilla Pablo 
Published: March 2022

AbstractAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive death of motor neurons and muscle atrophy, with defective neuron-glia interplay and emergence of aberrant glial phenotypes having a role in disease pathology. Here, we have studied if the pigment violacein with several reported protective/antiproliferative properties may control highly neurotoxic astrocytes (AbAs) obtained from spinal cord cultures of symptomatic hSOD1G93A rats, and if it could be neuroprotective in this ALS experimental model. At concentrations lower than those reported as protective, violacein selectively killed aberrant astrocytes. Treatment of hSOD1G93A rats with doses equivalent to the concentrations that killed AbAs caused a marginally significant delay in survival, partially preserved the body weight and soleus muscle mass and improved the integrity of the neuromuscular junction. Reduced motor neuron death and glial reactivity was also found and likely related to decreased inflammation and matrix metalloproteinase-2 and -9. Thus, in spite that new experimental designs aimed at extending the lifespan of hSOD1G93A rats are needed, improvements observed upon violacein treatment suggest a significant therapeutic potential that deserves further studies.
Giant paleo-seafloor craters and mass wasting associated with magma-induced uplift of the upper crust
Authors: Omosanya K. O. , Duffaut K. , Alves T. M. , Eruteya O. E. , Johansen S. E. , Waldmann N. 
Published: March 2022

AbstractGiant seafloor craters are known along many a continental margin with recurrent mass-wasting deposits. However, the impact of breakup-related magmatism on the evolution of such craters is barely understood. Using high-quality geophysical datasets, this work examines the genetic relationship among the location of magmatic sills, forced folds and the formation of giant paleo-seafloor craters underneath an ancient mass-transport complex in the Møre and Vøring basins, offshore Norway. The data reveal that forced folding of near-seafloor strata occurred because of the intrusion of several interconnected magmatic sills. Estimates of 1-dimensional uplift based on well data show that uplift occurred due to the intrusion of magma in Upper Cretaceous to Lower Eocene strata. Our findings also prove that subsurface fluid plumbing associated with the magmatic sills was prolonged in time and led to the development of several vertical fluid flow conduits, some of which triggered mass wasting in Neogene to Recent times. The repeated vertical expulsion of subsurface fluids weakened the strata on the continental slope, thereby promoting mass wasting, the selective cannibalization of the paleo-seafloor, and the formation of elongated craters at the basal shear zone of the mass-transport complex. Significantly, the model presented here proves a close link between subsurface magmatic plumbing systems and mass wasting on continental margins.
Metabolic plasticity improves lobster’s resilience to ocean warming but not to climate-driven novel species interactions
Authors: Oellermann Michael , Fitzgibbon Quinn P. , Twiname Samantha , Pecl Gretta T. 
Published: March 2022

AbstractMarine species not only suffer from direct effects of warming oceans but also indirectly via the emergence of novel species interactions. While metabolic adjustments can be crucial to improve resilience to warming, it is largely unknown if this improves performance relative to novel competitors. We aimed to identify if spiny lobsters—inhabiting a global warming and species re-distribution hotspot—align their metabolic performance to improve resilience to both warming and novel species interactions. We measured metabolic and escape capacity of two Australian spiny lobsters, resident Jasus edwardsii and the range-shifting Sagmariasus verreauxi, acclimated to current average—(14.0 °C), current summer—(17.5 °C) and projected future summer—(21.5 °C) habitat temperatures. We found that both species decreased their standard metabolic rate with increased acclimation temperature, while sustaining their scope for aerobic metabolism. However, the resident lobster showed reduced anaerobic escape performance at warmer temperatures and failed to match the metabolic capacity of the range-shifting lobster. We conclude that although resident spiny lobsters optimise metabolism in response to seasonal and future temperature changes, they may be unable to physiologically outperform their range-shifting competitors. This highlights the critical importance of exploring direct as well as indirect effects of temperature changes to understand climate change impacts.
Synergistic effects of carvacrol, α-terpinene, γ-terpinene, ρ-cymene and linalool against Gardnerella species
Authors: Sousa Lúcia G. V. , Castro Joana , Cavaleiro Carlos , Salgueiro Lígia , Tomás Mariana , Palmeira-Oliveira Rita , Martinez-Oliveira José , Cerca Nuno 
Published: March 2022

AbstractBacterial vaginosis (BV) is the most common vaginal infection affecting women worldwide. This infection is characterized by the loss of the dominant Lactobacillus community in the vaginal microbiota and an increase of anaerobic bacteria, that leads to the formation of a polymicrobial biofilm, mostly composed of Gardnerella spp. Treatment of BV is normally performed using broad-spectrum antibiotics, such as metronidazole and clindamycin. However, the high levels of recurrence of infection after treatment cessation have led to a demand for new therapeutic alternatives. Thymbra capitata essential oils (EOs) are known to have a wide spectrum of biological properties, including antibacterial activity. Thus, herein, we characterized two EOs of T. capitata and tested their antimicrobial activity as well as some of their main components, aiming to assess possible synergistic effects. Our findings showed that carvacrol and ρ-cymene established a strong synergistic antimicrobial effect against planktonic cultures of Gardnerella spp. On biofilm, carvacrol and linalool at sub-MIC concentrations proved more efficient in eliminating biofilm cells, while showing no cytotoxicity observed in a reconstituted human vaginal epithelium. The antibiofilm potential of the EOs and compounds was highlighted by the fact cells were not able to recover culturability after exposure to fresh medium.
A genetic risk score of alleles related to MGUS interacts with socioeconomic position in a population-based cohort
Authors: Baak Lisa , Frank Mirjam , Dürig Jan , Dührsen Ulrich , Hoffmann Per , Nöthen Markus M. , Dragano Nico , Erbel Raimund , Jöckel Karl-Heinz , Schmidt Börge 
Published: March 2022

AbstractEnvironmental, genetic, and social factors are suggested to jointly influence monoclonal gammopathy of undetermined significance (MGUS), a precursor of multiple myeloma. Aim of this study was to investigate interactions between MGUS-related genetic variants and socioeconomic position (SEP) indicators education and income on MGUS in a population-based study. Two different MGUS-related genetic risk allele sum scores (GRS) were calculated based on recent genome-wide meta-analyses. Odds Ratios (OR) were estimated in 4329 participants including 238 MGUS cases to assess associations and multiplicative interaction. The relative excess risk due to interaction (RERI) was calculated to assess additive interaction. Both GRSs were associated with MGUS. A multiplicative interaction between one GRS and education was observed with genetic effects of OR 1.34 (95% CI 1.11–1.62) per risk allele in the highest and OR 1.06 (95% CI 0.86–1.31) in the lowest education group. A RERI of 0.10 (95% CI 0.05–0.14) also indicated additive interaction. Further, additive GRS by income interaction (RERI 0.07; 95% CI 0.01–0.13) for the same GRS was also indicated. Results indicate interaction between MGUS-related genetic risk and SEP. Non-genetic MGUS risk factors more common in higher education groups may influence the expression of MGUS-related genetic variants.
Ceftolozane/tazobactam versus colistin in the treatment of ventilator-associated pneumonia due to extensively drug-resistant Pseudomonas aeruginosa
Authors: Mogyoródi Bence , Csékó András B. , Hermann Csaba , Gál János , Iványi Zsolt D. 
Published: March 2022

AbstractResistant strains of Pseudomonas aeruginosa are common pathogens in the intensive care unit (ICU), limiting available therapeutic options. We aimed to compare ceftolozane/tazobactam (C/T) with colistimethate sodium (CMS) in the treatment of ventilator-associated pneumonia (VAP) due to extensively drug-resistant (XDR) Pseudomonas aeruginosa. A retrospective, observational study was performed at a tertiary care ICU. Clinical and microbiological success rate, 28-day all-cause mortality, and adverse events were compared in patients who received C/T with those treated with systemic CMS. A total of 51 patients were included (18 in the C/T and 33 in the CMS group). Clinical success rates in the C/T and CMS groups were 13 (72.2%) and 10 (30.3%), respectively. On multivariate regression analysis, treatment with C/T was independently associated with clinical success (odds ratio 4.47, 95% CI 1.17–17.08). There was no difference in 28-day all-cause mortality (27.8% and 33.3% in the C/T and CMS group, p = 0.76). Acute kidney injury was more common in patients who received CMS (48.5% vs 11.1%, p = 0.01). In our study, ceftolozane/tazobactam was more efficacious in the treatment of XDR Pseudomonas aeruginosa VAP and showed a better safety profile compared to CMS.
Interpretable EEG seizure prediction using a multiobjective evolutionary algorithm
Authors: Pinto Mauro , Coelho Tiago , Leal Adriana , Lopes Fábio , Dourado António , Martins Pedro , Teixeira César 
Published: March 2022

AbstractSeizure prediction might be the solution to tackle the apparent unpredictability of seizures in patients with drug-resistant epilepsy, which comprise about a third of all patients with epilepsy. Designing seizure prediction models involves defining the pre-ictal period, a transition stage between inter-ictal brain activity and the seizure discharge. This period is typically a fixed interval, with some recent studies reporting the evaluation of different patient-specific pre-ictal intervals. Recently, researchers have aimed to determine the pre-ictal period, a transition stage between regular brain activity and a seizure. Authors have been using deep learning models given the ability of such models to automatically perform pre-processing, feature extraction, classification, and handling temporal and spatial dependencies. As these approaches create black-box models, clinicians may not have sufficient trust to use them in high-stake decisions. By considering these problems, we developed an evolutionary seizure prediction model that identifies the best set of features while automatically searching for the pre-ictal period and accounting for patient comfort. This methodology provides patient-specific interpretable insights, which might contribute to a better understanding of seizure generation processes and explain the algorithm’s decisions. We tested our methodology on 238 seizures and 3687 h of continuous data, recorded on scalp recordings from 93 patients with several types of focal and generalised epilepsies. We compared the results with a seizure surrogate predictor and obtained a performance above chance for 32% patients. We also compared our results with a control method based on the standard machine learning pipeline (pre-processing, feature extraction, classifier training, and post-processing), where the control marginally outperformed our approach by validating 35% of the patients. In total, 54 patients performed above chance for at least one method: our methodology or the control one. Of these 54 patients, 21 ($$\approx$$
≈
38%) were solely validated by our methodology, while 24 ($$\approx$$
≈
44%) were only validated by the control method. These findings may evidence the need for different methodologies concerning different patients.
The different overall survival between single-agent EGFR-TKI treatment and with bevacizumab in non-small cell lung cancer patients with brain metastasis
Authors: Chiu Tzu-Hsuan , Tung Pi-Hung , Huang Chi-Hsien , Ju Jia-Shiuan , Huang Allen Chung-Cheng , Wang Chin-Chou , Ko Ho-Wen , Hsu Ping-Chih , Fang Yueh-Fu , Guo Yi-Ke , Kuo Chih-Hsi Scott , Yang Cheng-Ta 
Published: March 2022

AbstractComparison of epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) monotherapy or with bevacizumab in real-world non-small cell lung cancer (NSCLC) patients was lacking. 310 patients of advanced NSCLC with common EGFR mutation receiving first-generation EGFR-TKI monotherapy or with bevacizumab were included and propensity-score matched. Progression-free survival (PFS), overall survival (OS) and secondary T790M mutation were analysed. Patients receiving EGFR-TKI and bevacizumab were significantly younger, had better performance status and with high incidence of brain metastasis (55.8%). In the propensity-score matched cohort, PFS (13.5 vs. 13.7 months; log-rank p = 0.700) was similar between the two groups. The OS (61.3 vs. 34.2 months; log-rank p = 0.010) and risk reduction of death (HR 0.42 [95% CI 0.20–0.85]; p = 0.017) were significantly improved in EGFR-TKI plus bevacizumab group. Analysis of treatment by brain metastasis status demonstrated EGFR-TKI plus bevacizumab in patients with brain metastasis was associated with significant OS benefit compared to other groups (log-rank p = 0.030) and these patients had lower early-CNS and early-systemic progressions. The secondary T790M did not significantly differ between EGFR-TKI plus bevacizumab and EGFR-TKI monotherapy groups (66.7% vs. 75.0%, p = 0.460). Forty-one (31.1%) and 31 (23.5%) patients received subsequent osimertinib and chemotherapy, respectively. The post-progression OS of osimertinib and chemotherapy were 22.1 and 44.9 months in EGFR-TKI plus bevacizumab group and were 10.0 and 14.1 months in EGFR-TKI monotherpay group, respectively. First-generation EGFR-TKI with bevacizumab improved treatment efficacy in real-world patients of NSCLC with EGFR mutation. Patients with brain metastasis received additional OS benefit from this treatment.
The possible role of hypoxia in the affected tissue of relapsed clubfoot
Authors: Novotny Tomas , Eckhardt Adam , Doubkova Martina , Knitlova Jarmila , Vondrasek David , Vanaskova Eliska , Ostadal Martin , Uhlik Jiri , Bacakova Lucie , Musilkova Jana 
Published: March 2022

AbstractOur aim was to study the expression of hypoxia-related proteins as a possible regulatory pathway in the contracted side tissue of relapsed clubfoot. We compared the expression of hypoxia-related proteins in the tissue of the contracted (medial) side of relapsed clubfoot, and in the tissue of the non-contracted (lateral) side of relapsed clubfoot. Tissue samples from ten patients were analyzed by immunohistochemistry and image analysis, Real-time PCR and Mass Spectrometry to evaluate the differences in protein composition and gene expression. We found a significant increase in the levels of smooth muscle actin, transforming growth factor-beta, hypoxia-inducible factor 1 alpha, lysyl oxidase, lysyl oxidase-like 2, tenascin C, matrix metalloproteinase-2, matrix metalloproteinase-9, fibronectin, collagen types III and VI, hemoglobin subunit alpha and hemoglobin subunit beta, and an overexpression of ACTA2, FN1, TGFB1, HIF1A and MMP2 genes in the contracted medial side tissue of clubfoot. In the affected tissue, we have identified an increase in the level of hypoxia-related proteins, together with an overexpression of corresponding genes. Our results suggest that the hypoxia-associated pathway is potentially a factor contributing to the etiology of clubfoot relapses, as it stimulates both angioproliferation and fibroproliferation, which are considered to be key factors in the progression and development of relapses.
Dispersive and dissipative coupling of photon Bose-Einstein condensates
Authors: Toebes Chris , Vretenar Mario , Klaers Jan 
Published: March 2022

AbstractThe synchronization of coherent states of light has long been an important subject of basic research and technology. Recently, a new concept for analog computers has emerged where this synchronization process can be exploited to solve computationally hard problems - potentially faster and more energy-efficient than what can be achieved with conventional computer technology today. The unit cell of such systems consists of two coherent centers that are coupled to one another in a controlled manner. Here, we experimentally characterize and analyze the synchronization process of two photon Bose-Einstein condensates, which are coupled to one another, either dispersively or dissipatively. We show that both types of coupling are robust against a detuning of the condensate frequencies and show similar time constants in establishing mutual coherence. Significant differences between these couplings arise in the behaviour of the condensate populations under imbalanced optical pumping. The combination of these two types of coupling extends the class of physical models that can be investigated using analog simulations.