bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iron mineral dissolution releases iron and associated organic carbon during permafrost thaw
Authors: Patzner Monique S. , Mueller Carsten W. , Malusova Miroslava , Baur Moritz , Nikeleit Verena , Scholten Thomas , Hoeschen Carmen , Byrne James M. , Borch Thomas , Kappler Andreas , Bryce Casey 
Published: December 2020

AbstractIt has been shown that reactive soil minerals, specifically iron(III) (oxyhydr)oxides, can trap organic carbon in soils overlying intact permafrost, and may limit carbon mobilization and degradation as it is observed in other environments. However, the use of iron(III)-bearing minerals as terminal electron acceptors in permafrost environments, and thus their stability and capacity to prevent carbon mobilization during permafrost thaw, is poorly understood. We have followed the dynamic interactions between iron and carbon using a space-for-time approach across a thaw gradient in Abisko (Sweden), where wetlands are expanding rapidly due to permafrost thaw. We show through bulk (selective extractions, EXAFS) and nanoscale analysis (correlative SEM and nanoSIMS) that organic carbon is bound to reactive Fe primarily in the transition between organic and mineral horizons in palsa underlain by intact permafrost (41.8 ± 10.8 mg carbon per g soil, 9.9 to 14.8% of total soil organic carbon). During permafrost thaw, water-logging and O2limitation lead to reducing conditions and an increase in abundance of Fe(III)-reducing bacteria which favor mineral dissolution and drive mobilization of both iron and carbon along the thaw gradient. By providing a terminal electron acceptor, this rusty carbon sink is effectively destroyed along the thaw gradient and cannot prevent carbon release with thaw.
Human gingival fibroblast secretome accelerates wound healing through anti-inflammatory and pro-angiogenic mechanisms
Authors: Ahangar Parinaz , Mills Stuart J. , Smith Louise E. , Gronthos Stan , Cowin Allison J. 
Published: December 2020

AbstractHealing of the skin and oral mucosa utilises similar mechanisms of tissue repair, however, scarring and the rate of wound closure is vastly superior in the oral cavity suggesting differences between these two environments. One key difference is the phenotype of dermal fibroblasts compared to fibroblasts of gingival tissues. Human gingival fibroblasts (hGFs) are undifferentiated cells with multi-differentiation and self-renewal capacities. This study aimed to examine if delivering hGFs or their secretome, contained in hGF-conditioned media (hGF-CM), would improve healing of the skin and recapitulate features of oral healing. Human fibroblasts, keratinocytes and endothelial cells were first treated with hGF-CM and showed improved migration, proliferation and angiogenic functions. A significant reduction in macroscopic wound area and histologic dermal wound width, as well as an increased rate of re-epithelialisation, were observed in both hGFs and hGF-CM treated murine excisional wounds. This improvement was associated with reduced inflammation, increased angiogenesis and elevated collagen deposition. These findings demonstrate that treatment of dermal wounds with either hGFs or hGF-CM may provide beneficial gingival-like properties to dermal wounds and may be a potential opportunity for improving healing of the skin.
Public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden
Authors: Mondino Elena , Di Baldassarre Giuliano , Mård Johanna , Ridolfi Elena , Rusca Maria 
Published: December 2020

AbstractKnowing how people perceive multiple risks is essential to the management and promotion of public health and safety. Here we present a dataset based on a survey (N = 4,154) of public risk perception in Italy and Sweden during the COVID-19 pandemic. Both countries were heavily affected by the first wave of infections in Spring 2020, but their governmental responses were very different. As such, the dataset offers unique opportunities to investigate the role of governmental responses in shaping public risk perception. In addition to epidemics, the survey considered indirect effects of COVID-19 (domestic violence, economic crises), as well as global (climate change) and local (wildfires, floods, droughts, earthquakes, terror attacks) threats. The survey examines perceived likelihoods and impacts, individual and authorities’ preparedness and knowledge, and socio-demographic indicators. Hence, the resulting dataset has the potential to enable a plethora of analyses on social, cultural and institutional factors influencing the way in which people perceive risk.
A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis
Authors: Porcellato Davide , Meisal Roger , Bombelli Alberto , Narvhus Judith A. 
Published: December 2020

AbstractThe importance of the microbiome for bovine udder health is not well explored and most of the knowledge originates from research on mastitis. Better understanding of the microbial diversity inside the healthy udder of lactating cows might help to reduce mastitis, use of antibiotics and improve animal welfare. In this study, we investigated the microbial diversity of over 400 quarter milk samples from 60 cows sampled from two farms and on two different occasions during the same lactation period. Microbiota analysis was performed using amplicon sequencing of the 16S rRNA gene and over 1000 isolates were identified using MALDI-TOF MS. We detected a high abundance of two bacterial families, Corynebacteriaceae and Staphylococcaceae, which accounted for almost 50% of the udder microbiota of healthy cows and were detected in all the cow udders and in more than 98% of quarter milk samples. A strong negative correlation between these bacterial families was detected indicating a possible competition. The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow. Furthermore, we introduced a novel definition of a dysbiotic quarter at individual cow level, by analyzing the milk microbiota, and a high frequency of dysbiotic quarter samples were detected distributed among the farms and the samples. These results emphasize the importance of deepening the studies of the bovine udder microbiome to elucidate its role in udder health.
Automatic segmentation with detection of local segmentation failures in cardiac MRI
Authors: Sander Jörg , de Vos Bob D. , Išgum Ivana 
Published: December 2020

AbstractSegmentation of cardiac anatomical structures in cardiac magnetic resonance images (CMRI) is a prerequisite for automatic diagnosis and prognosis of cardiovascular diseases. To increase robustness and performance of segmentation methods this study combines automatic segmentation and assessment of segmentation uncertainty in CMRI to detect image regions containing local segmentation failures. Three existing state-of-the-art convolutional neural networks (CNN) were trained to automatically segment cardiac anatomical structures and obtain two measures of predictive uncertainty: entropy and a measure derived by MC-dropout. Thereafter, using the uncertainties another CNN was trained to detect local segmentation failures that potentially need correction by an expert. Finally, manual correction of the detected regions was simulated in the complete set of scans of 100 patients and manually performed in a random subset of scans of 50 patients. Using publicly available CMR scans from the MICCAI 2017 ACDC challenge, the impact of CNN architecture and loss function for segmentation, and the uncertainty measure was investigated. Performance was evaluated using the Dice coefficient, 3D Hausdorff distance and clinical metrics between manual and (corrected) automatic segmentation. The experiments reveal that combining automatic segmentation with manual correction of detected segmentation failures results in improved segmentation and to 10-fold reduction of expert time compared to manual expert segmentation.
The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals
Authors: Singh Parul , Rawat Arun , Alwakeel Mariam , Sharif Elham , Al Khodor Souhaila 
Published: December 2020

AbstractVitamin D deficiency affects approximately 80% of individuals in some countries and has been linked with gut dysbiosis and inflammation. While the benefits of vitamin D supplementation on the gut microbiota have been studied in patients with chronic diseases, its effects on the microbiota of otherwise healthy individuals is unclear. Moreover, whether effects on the microbiota can explain some of the marked inter-individual variation in responsiveness to vitamin D supplementation is unknown. Here, we administered vitamin D to 80 otherwise healthy vitamin D-deficient women, measuring serum 25(OH) D levels in blood and characterizing their gut microbiota pre- and post- supplementation using 16S rRNA gene sequencing. Vitamin D supplementation significantly increased gut microbial diversity. Specifically, the Bacteroidetes to Firmicutes ratio increased, along with the abundance of the health-promoting probiotic taxa Akkermansia and Bifidobacterium. Significant variations in the two-dominant genera, Bacteroides and Prevotella, indicated a variation in enterotypes following supplementation. Comparing supplementation responders and non-responders we found more pronounced changes in abundance of major phyla in responders, and a significant decrease in Bacteroides acidifaciens in non-responders. Altogether, our study highlights the positive impact of vitamin D supplementation on the gut microbiota and the potential for the microbial gut signature to affect vitamin D response.
In-situ quantification of microscopic contributions of individual cells to macroscopic wood deformation with synchrotron computed tomography
Authors: Sanabria Sergio J. , Baensch Franziska , Zauner Michaela , Niemz Peter 
Published: December 2020

AbstractWood-based composites hold the promise of sustainable construction. Understanding the influence on wood cellular microstructure in the macroscopic mechanical behavior is key for engineering high-performance composites. In this work, we report a novel Individual Cell Tracking (ICT) approach for in-situ quantification of nanometer-scale deformations of individual wood cells during mechanical loading of macroscopic millimeter-scale wood samples. Softwood samples containing > 104 cells were subjected to controlled radial tensile and longitudinal compressive load in a synchrotron radiation micro-computed tomography (SRµCT) setup. Tracheid and wood ray cells were automatically segmented, and their geometric variations were tracked during load. Finally, interactions between microstructure deformations (lumen geometry, cell wall thickness), cellular arrangement (annual growth rings, anisotropy, wood ray presence) with the macroscopic deformation response were investigated. The results provide cellular insight into macroscopic relations, such as anisotropic Poisson effects, and allow direct observation of previously suspected wood ray reinforcing effects. The method is also appropriate for investigation of non-linear deformation effects, such as buckling and deformation recovery after failure, and gives insight into less studied aspects, such as changes in lumen diameter and cell wall thickness during uniaxial load. ICT provides an experimental tool for direct validation of hierarchical mechanical models on real biological composites.
Risk factors and mortality in patients with pneumonia and elevated troponin levels
Authors: Efros Orly , Soffer Shelly , Leibowitz Avshalom , Fardman Alexander , Klempfner Robert , Meisel Eshcar , Grossman Ehud 
Published: December 2020

AbstractPneumonia in hospitalized patients is associated with myocardial injury. In this study, we evaluated risk factors for myocardial injury in hospitalized patients with pneumonia and its prognostic value. We retrieved all patients who were hospitalized in internal medicine departments in a tertiary medical center between 2008 and 2019 with a diagnosis of pneumonia. From 2008 to 2019 a total of 20,683 adult patients were hospitalized in internal medicine wards in the Sheba Medical Center with a diagnosis of pneumonia, 8195 were tested for troponin levels, and 3207 had elevated levels. Risk factors for elevated troponin levels were age, prior diagnosis of ischemic heart disease, and elevated creatinine level upon admission. The in-hospital mortality and 1-year mortality rate were higher among patients who had elevated troponin levels when using a propensity score-based matched analysis. In conclusion, in hospitalized patients with pneumonia elevated troponin levels have a major impact on prognosis. Hence, troponin levels may be used as another tool of risk stratification for patients hospitalized with pneumonia.
Analysis of enteric nervous system and intestinal epithelial barrier to predict complications in Hirschsprung’s disease
Authors: Dariel Anne , Grynberg Lucie , Auger Marie , Lefèvre Chloé , Durand Tony , Aubert Philippe , Le Berre-Scoul Catherine , Venara Aurélien , Suply Etienne , Leclair Marc-David , de Vries Philine , Levard Guillaume , Parmentier Benoit , Podevin Guillaume , Schmitt Françoise , Couvrat Véronique , Irtan Sabine , Hervieux Erik , Villemagne Thierry , Lardy Hubert , Capito Carmen , Muller Cécile , Sarnacki Sabine , Mosnier Jean-François , Galmiche Louise , Derkinderen Pascal , Boudin Hélène , Brochard Charlène , Neunlist Michel 
Published: December 2020

AbstractIn Hirschsprung’s disease (HSCR), postoperative course remains unpredictable. Our aim was to define predictive factors of the main postoperative complications: obstructive symptoms (OS) and Hirschsprung-associated enterocolitis (HAEC). In this prospective multicentre cohort study, samples of resected bowel were collected at time of surgery in 18 neonates with short-segment HSCR in tertiary care hospitals. OS and HAEC were noted during postoperative follow-up. We assessed the enteric nervous system and the intestinal epithelial barrier (IEB) in ganglionic segments by combining immunohistochemical, proteomic and transcriptomic approaches, with functional ex vivo analysis of motility and para/transcellular permeability. Ten HSCR patients presented postoperative complications (median follow-up 23.5 months): 6 OS, 4 HAEC (2 with OS), 2 diarrhoea (without OS/HAEC). Immunohistochemical analysis showed a significant 41% and 60% decrease in median number of nNOS-IR myenteric neurons per ganglion in HSCR with OS as compared to HSCR with HAEC/diarrhoea (without OS) and HSCR without complications (p = 0.0095; p = 0.002, respectively). Paracellular and transcellular permeability was significantly increased in HSCR with HAEC as compared to HSCR with OS/diarrhoea without HAEC (p = 0.016; p = 0.009) and HSCR without complications (p = 0.029; p = 0.017). This pilot study supports the hypothesis that modulating neuronal phenotype and enhancing IEB permeability may treat or prevent postoperative complications in HSCR.
Multi-omic approach provides insights into osmoregulation and osmoconformation of the crab Scylla paramamosain
Authors: Niu Jiaojiao , Hu Xue Lei , Ip Jack C. H. , Ma Ka Yan , Tang Yuanyuan , Wang Yaqin , Qin Jing , Qiu Jian-Wen , Chan Ting Fung , Chu Ka Hou 
Published: December 2020

AbstractOsmoregulation and osmoconformation are two mechanisms through which aquatic animals adapt to salinity fluctuations. The euryhaline crabScylla paramamosain,being both an osmoconformer and osmoregulator, is an excellent model organism to investigate salinity adaptation mechanisms in brachyurans. In the present study, we used transcriptomic and proteomic approaches to investigate the response ofS. paramamosainto salinity stress. Crabs were transferred from a salinity of 25 ppt to salinities of 5 ppt or 33 ppt for 6 h and 10 days. Data from both approaches revealed that exposure to 5 ppt resulted in upregulation of ion transport and energy metabolism associated genes. Notably, acclimation to low salinity was associated with early changes in gene expression for signal transduction and stress response. In contrast, exposure to 33 ppt resulted in upregulation of genes related to amino acid metabolism, and amino acid transport genes were upregulated only at the early stage of acclimation to this salinity. Our study reveals contrasting mechanisms underlying osmoregulation and osmoconformation within the salinity range of 5–33 ppt in the mud crab, and provides novel candidate genes for osmotic signal transduction, thereby providing insights on understanding the salinity adaptation mechanisms of brachyuran crabs.
Saturated fatty acids induce insulin resistance in podocytes through inhibition of IRS1 via activation of both IKKβ and mTORC1
Authors: Denhez Benoit , Rousseau Marina , Spino Crysta , Dancosst David-Alexandre , Dumas Marie-Ève , Guay Andréanne , Lizotte Farah , Geraldes Pedro 
Published: December 2020

AbstractDiabetic nephropathy (DN), a microvascular complication of diabetes, is the leading cause of end-stage renal disease worldwide. Multiple studies have shown that podocyte dysfunction is a central event in the progression of the disease. Beside chronic hyperglycemia, dyslipidemia can induce insulin resistance and dysfunction in podocytes. However, the exact mechanisms of free fatty acid (FFA)-induced podocyte insulin unresponsiveness are poorly understood. We used a type 2 diabetic mouse model (db/db) and mouse podocytes exposed to palmitic acid for 24 h followed by an insulin stimulation. Renal function and pathology were evaluated at 25 weeks of age to confirm the DN development. Our results demonstrate that saturated FFA activated the serine/threonine kinases IκB kinase (IKK)β/IκBα and mTORC1/S6K1, but not protein kinase C and c-jun N-terminal kinase, in podocytes and glomeruli of db/db mice. Activation of both kinases promoted serine 307 phosphorylation of IRS1, a residue known to provoke IRS1 inhibition. Using IKK, mTORC1 and ceramide production inhibitors, we were able to blunt IRS1 serine 307 phosphorylation and restore insulin stimulation of Akt. In conclusion, our results indicate that FFA and diabetes contribute to insulin resistance through the activation of IKKβ and S6K1 leading to podocyte dysfunction and DN.
Beta-hydroxybutyrate, an endogenous NLRP3 inflammasome inhibitor, attenuates anxiety-related behavior in a rodent post-traumatic stress disorder model
Authors: Yamanashi Takehiko , Iwata Masaaki , Shibushita Midori , Tsunetomi Kyohei , Nagata Mayu , Kajitani Naofumi , Miura Akihiko , Matsuo Ryoichi , Nishiguchi Tsuyoshi , Kato Takahiro A. , Setoyama Daiki , Shirayama Yukihiko , Watanabe Ken , Shinozaki Gen , Kaneko Koichi 
Published: December 2020

AbstractAccumulating evidence suggests that elevated inflammation contributes to the pathophysiology of post-traumatic stress disorder (PTSD) and that anti-inflammatory drugs might be a new treatment strategy for PTSD. It has been reported that beta-hydroxybutyrate (BHB), one of the main ketone bodies produced, can have an anti-inflammatory and antidepressant effect. Here, we investigated the potential anti-anxiety and anti-inflammatory effects of BHB using a rodent PTSD model, induced by single prolonged stress (SPS). Male, Sprague–Dawley rats were employed in this study. Repeated administration of BHB attenuated SPS-induced anxiety-related behaviors evaluated by the elevated plus maze test. SPS increased the serum levels of TNF-α and IL-1β. In contrast, BHB administration partially attenuated the increase of serum TNF-α. These findings demonstrate that BHB exerts its anxiolytic effects, possibly by inhibiting systemic TNF-α. Hence, BHB may be a novel therapeutic candidate for the treatment of PTSD.
Systematic review and meta-analysis of the associations of vegan and vegetarian diets with inflammatory biomarkers
Authors: Menzel Juliane , Jabakhanji Afraa , Biemann Ronald , Mai Knut , Abraham Klaus , Weikert Cornelia 
Published: December 2020

AbstractPlant-based diets like vegetarian or vegan diets might influence circulating levels of inflammatory biomarkers, thereby reducing the risk of chronic diseases. This systematic review and meta-analysis aimed to investigate the associations of veganism and vegetarianism with circulating inflammatory biomarkers in comparison to omnivores. Literature search was conducted in Pubmed and EMBASE until April 2020 and mean differences of biomarkers were assessed for: C-reactive protein (CRP), interleukin-6 (IL-6), interleukin-18 (IL-18), interleukin-1 receptor antagonist (IL-1 RA), tumor necrosis factor-alpha (TNF-ɑ), E-selectin, intercellular adhesion molecule-1 (ICAM-1), monocyte chemoattractant protein-1 (MCP-1), adiponectin, omentin-1 and resistin. Of initially identified 1073 publications, 21 cross-sectional studies met the inclusion criteria and were included in the systematic review and meta-analysis. Vegan diet was associated with lower levels of CRP compared to omnivores [mean difference − 0.54 mg/l, 95%-CI: − 0.79 to − 0.28, p < 0.0001]. This association was less pronounced in vegetarians [mean difference − 0.25 mg/l, 95%-CI: − 0.49 to 0.00, p = 0.05]. In patients with impaired kidney function, the association between vegetarian nutrition and CRP was much stronger with − 3.91 mg/l (95%-CI: − 5.23 to − 2.60; p < 0.0001). No substantial effects were observed for all other inflammatory biomarkers. Despite strong associations between CRP and a vegan or vegetarian diet were seen, further research is needed, as most inflammatory biomarkers were investigated only in single studies so far.
Production of the antimicrobial compound tetrabromopyrrole and the Pseudomonas quinolone system precursor, 2-heptyl-4-quinolone, by a novel marine species Pseudoalteromonas galatheae sp. nov.
Authors: Paulsen Sara Skøtt , Isbrandt Thomas , Kirkegaard Markus , Buijs Yannick , Strube Mikael Lenz , Sonnenschein Eva C. , Larsen Thomas O. , Gram Lone 
Published: December 2020

AbstractNovel antimicrobials are urgently needed due to the rapid spread of antibiotic resistant bacteria. In a genome-wide analysis of Pseudoalteromonas strains, one strain (S4498) was noticed due to its potent antibiotic activity. It did not produce the yellow antimicrobial pigment bromoalterochromide, which was produced by several related type strains with which it shared less than 95% average nucleotide identity. Also, it produced a sweet-smelling volatile not observed from other strains. Mining the genome of strain S4498 using the secondary metabolite prediction tool antiSMASH led to eight biosynthetic gene clusters with no homology to known compounds, and synteny analyses revealed that the yellow pigment bromoalterochromide was likely lost during evolution. Metabolome profiling of strain S4498 using HPLC-HRMS analyses revealed marked differences to the type strains. In particular, a series of quinolones known as pseudanes were identified and verified by NMR. The characteristic odor of the strain was linked to the pseudanes. The highly halogenated compound tetrabromopyrrole was detected as the major antibacterial component by bioassay-guided fractionation. Taken together, the polyphasic analysis demonstrates that strain S4498 belongs to a novel species within the genus Pseudoalteromonas, and we propose the name Pseudoalteromonas galatheae sp. nov. (type strain S4498T = NCIMB 15250T = LMG 31599T).