bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical activity and the risk of abdominal aortic aneurysm: a systematic review and meta-analysis of prospective studies
Authors: Aune Dagfinn , Sen Abhijit , Kobeissi Elsa , Hamer Mark , Norat Teresa , Riboli Elio 
Published: December 2020

AbstractThe association between physical activity and risk of abdominal aortic aneurysm has been inconsistent with some studies reporting a reduced risk while others have found no association. We conducted a systematic review and meta-analysis of prospective studies to quantify the association. PubMed and Embase databases were searched up to 3 October 2020. Prospective studies were included if they reported adjusted relative risk (RR) estimates and 95% confidence intervals (CIs) of abdominal aortic aneurysm associated with physical activity. Summary RRs (95% CIs) were estimated using a random effects model. Nine prospective studies (2073 cases, 409,732 participants) were included. The summary RR for high vs. low physical activity was 0.70 (95% CI: 0.56–0.87, I2 = 58%) and per 20 metabolic equivalent task (MET)-hours/week increase of activity was 0.84 (95% CI: 0.74–0.95, I2 = 59%, n = 6). Although the test for nonlinearity was not significant (p = 0.09) the association appeared to be stronger when increasing the physical activity level from 0 to around 20–25 MET-hours/week than at higher levels. The current meta-analysis suggest that higher physical activity may reduce the risk of abdominal aortic aneurysm, however, further studies are needed to clarify the dose–response relationship between different subtypes and intensities of activity and abdominal aortic aneurysm risk.
Bumble bees in landscapes with abundant floral resources have lower pathogen loads
Authors: McNeil Darin J. , McCormick Elyse , Heimann Ashley C. , Kammerer Melanie , Douglas Margaret R. , Goslee Sarah C. , Grozinger Christina M. , Hines Heather M. 
Published: December 2020

AbstractThe pollination services provided by bees are essential for supporting natural and agricultural ecosystems. However, bee population declines have been documented across the world. Many of the factors known to undermine bee health (e.g., poor nutrition) can decrease immunocompetence and, thereby, increase bees’ susceptibility to diseases. Given the myriad of stressors that can exacerbate disease in wild bee populations, assessments of the relative impact of landscape habitat conditions on bee pathogen prevalence are needed to effectively conserve pollinator populations. Herein, we assess how landscape-level conditions, including various metrics of floral/nesting resources, insecticides, weather, and honey bee (Apis mellifera) abundance, drive variation in wild bumble bee (Bombus impatiens) pathogen loads. Specifically, we screened 890 bumble bee workers from varied habitats in Pennsylvania, USA for three pathogens (deformed wing virus, black queen cell virus, and Vairimorpha (= Nosema) bombi), Defensin expression, and body size. Bumble bees collected within low-quality landscapes exhibited the highest pathogen loads, with spring floral resources and nesting habitat availability serving as the main drivers. We also found higher loads of pathogens where honey bee apiaries are more abundant, a positive relationship between Vairimorpha loads and rainfall, and differences in pathogens by geographic region. Collectively, our results highlight the need to support high-quality landscapes (i.e., those with abundant floral/nesting resources) to maintain healthy wild bee populations.
Out of India, thrice: diversification of Asian forest scorpions reveals three colonizations of Southeast Asia
Authors: Loria Stephanie F. , Prendini Lorenzo 
Published: December 2020

AbstractThe ‘Out of India’ hypothesis is often invoked to explain patterns of distribution among Southeast Asian taxa. According to this hypothesis, Southeast Asian taxa originated in Gondwana, diverged from their Gondwanan relatives when the Indian subcontinent rifted from Gondwana in the Late Jurassic, and colonized Southeast Asia when it collided with Eurasia in the early Cenozoic. A growing body of evidence suggests these events were far more complex than previously understood, however. The first quantitative reconstruction of the biogeography of Asian forest scorpions (Scorpionidae Latreille, 1802: Heterometrinae Simon, 1879) is presented here. Divergence time estimation, ancestral range estimation, and diversification analyses are used to determine the origins, dispersal and diversification patterns of these scorpions, providing a timeline for their biogeographical history that can be summarized into four major events. (1) Heterometrinae diverged from other Scorpionidae on the African continent after the Indian subcontinent became separated in the Cretaceous. (2) Environmental stresses during the Cretaceous–Tertiary (KT) mass extinction caused range contraction, restricting one clade of Heterometrinae to refugia in southern India (the Western Ghats) and Sri Lanka (the Central Highlands). (3) Heterometrinae dispersed to Southeast Asia three times during India’s collision with Eurasia, the first dispersal event occurring as the Indian subcontinent brushed up against the western side of Sumatra, and the other two events occurring as India moved closer to Eurasia. (4) Indian Heterometrinae, confined to southern India and Sri Lanka during the KT mass extinction, recolonized the Deccan Plateau and northern India, diversifying into new, more arid habitats after environmental conditions stabilized. These hypotheses, which are congruent with the geological literature and biogeographical analyses of other taxa from South and Southeast Asia, contribute to an improved understanding of the dispersal and diversification patterns of taxa in this biodiverse and geologically complex region.
Evaluation of mutation rates, mosaicism and off target mutations when injecting Cas9 mRNA or protein for genome editing of bovine embryos
Authors: Hennig Sadie L. , Owen Joseph R. , Lin Jason C. , Young Amy E. , Ross Pablo J. , Van Eenennaam Alison L. , Murray James D. 
Published: December 2020

AbstractThe CRISPR/Cas9 genome editing tool has the potential to improve the livestock breeding industry by allowing for the introduction of desirable traits. Although an efficient and targeted tool, the CRISPR/Cas9 system can have some drawbacks, including off-target mutations and mosaicism, particularly when used in developing embryos. Here, we introduced genome editing reagents into single-cell bovine embryos to compare the effect of Cas9 mRNA and protein on the mutation efficiency, level of mosaicism, and evaluate potential off-target mutations utilizing next generation sequencing. We designed guide-RNAs targeting three loci (POLLED, H11, and ZFX) in the bovine genome and saw a significantly higher rate of mutation in embryos injected with Cas9 protein (84.2%) vs. Cas9 mRNA (68.5%). In addition, the level of mosaicism was higher in embryos injected with Cas9 mRNA (100%) compared to those injected with Cas9 protein (94.2%), with little to no unintended off-target mutations detected. This study demonstrated that the use of gRNA/Cas9 ribonucleoprotein complex resulted in a high editing efficiency at three different loci in bovine embryos and decreased levels of mosaicism relative to Cas9 mRNA. Additional optimization will be required to further reduce mosaicism to levels that make single-step embryo editing in cattle commercially feasible.
Discovery and validation of an NMR-based metabolomic profile in urine as TB biomarker
Authors: Izquierdo-Garcia José Luis , Comella-del-Barrio Patricia , Campos-Olivas Ramón , Villar-Hernández Raquel , Prat-Aymerich Cristina , De Souza-Galvão Maria Luiza , Jiménez-Fuentes Maria Angeles , Ruiz-Manzano Juan , Stojanovic Zoran , González Adela , Serra-Vidal Mar , García-García Esther , Muriel-Moreno Beatriz , Millet Joan Pau , Molina-Pinargote Israel , Casas Xavier , Santiago Javier , Sabriá Fina , Martos Carmen , Herzmann Christian , Ruiz-Cabello Jesús , Domínguez José 
Published: December 2020

AbstractDespite efforts to improve tuberculosis (TB) detection, limitations in access, quality and timeliness of diagnostic services in low- and middle-income countries are challenging for current TB diagnostics. This study aimed to identify and characterise a metabolic profile of TB in urine by high-field nuclear magnetic resonance (NMR) spectrometry and assess whether the TB metabolic profile is also detected by a low-field benchtop NMR spectrometer. We included 189 patients with tuberculosis, 42 patients with pneumococcal pneumonia, 61 individuals infected with latent tuberculosis and 40 uninfected individuals. We acquired the urine spectra from high and low-field NMR. We characterised a TB metabolic fingerprint from the Principal Component Analysis. We developed a classification model from the Partial Least Squares-Discriminant Analysis and evaluated its performance. We identified a metabolic fingerprint of 31 chemical shift regions assigned to eight metabolites (aminoadipic acid, citrate, creatine, creatinine, glucose, mannitol, phenylalanine, and hippurate). The model developed using low-field NMR urine spectra correctly classified 87.32%, 85.21% and 100% of the TB patients compared to pneumococcal pneumonia patients, LTBI and uninfected individuals, respectively. The model validation correctly classified 84.10% of the TB patients. We have identified and characterised a metabolic profile of TB in urine from a high-field NMR spectrometer and have also detected it using a low-field benchtop NMR spectrometer. The models developed from the metabolic profile of TB identified by both NMR technologies were able to discriminate TB patients from the rest of the study groups and the results were not influenced by anti-TB treatment or TB location. This provides a new approach in the search for possible biomarkers for the diagnosis of TB.
Cortical bone adaptation to a moderate level of mechanical loading in male Sost deficient mice
Authors: Yang Haisheng , Büttner Alexander , Albiol Laia , Julien Catherine , Thiele Tobias , Figge Christine , Kramer Ina , Kneissel Michaela , Duda Georg N. , Checa Sara , Willie Bettina M. 
Published: December 2020

AbstractLoss-of-function mutations in the Sost gene lead to high bone mass phenotypes. Pharmacological inhibition of Sost/sclerostin provides a new drug strategy for treating osteoporosis. Questions remain as to how physical activity may affect bone mass under sclerostin inhibition and if that effect differs between males and females. We previously observed in female Sost knockout (KO) mice an enhanced cortical bone formation response to a moderate level of applied loading (900 με at the tibial midshaft). The purpose of the present study was to examine cortical bone adaptation to the same strain level applied to male Sost KO mice. Strain-matched in vivo compressive loading was applied to the tibiae of 10-, 26- and 52-week-old male Sost KO and littermate control (LC) mice. The effect of tibial loading on bone (re)modeling was measured by microCT, 3D time-lapse in vivo morphometry, 2D histomorphometry and gene expression analyses. As expected, Sost deficiency led to high cortical bone mass in 10- and 26-week-old male mice as a result of increased bone formation. However, the enhanced bone formation associated with Sost deficiency did not appear to diminish with skeletal maturation. An increase in bone resorption was observed with skeletal maturation in male LC and Sost KO mice. Two weeks of in vivo loading (900 με at the tibial midshaft) induced only a mild anabolic response in 10- and 26-week-old male mice, independent of Sost deficiency. A decrease in the Wnt inhibitor Dkk1 expression was observed 3 h after loading in 52-week-old Sost KO and LC mice, and an increase in Lef1 expression was observed 8 h after loading in 10-week-old Sost KO mice. The current results suggest that long-term inhibition of sclerostin in male mice does not influence the adaptive response of cortical bone to moderate levels of loading. In contrast with our previous strain-matched study in females showing enhanced bone responses with Sost ablation, these results in males indicate that the influence of Sost deficiency on the cortical bone formation response to a moderate level of loading differs between males and females. Clinical studies examining antibodies to inhibit sclerostin may need to consider that the efficacy of additional physical activity regimens may be sex dependent.
The relationship between resting-state functional connectivity, antidepressant discontinuation and depression relapse
Authors: Berwian Isabel M. , Wenzel Julia G. , Kuehn Leonie , Schnuerer Inga , Kasper Lars , Veer Ilya M. , Seifritz Erich , Stephan Klaas E. , Walter Henrik , Huys Quentin J. M. 
Published: December 2020

AbstractThe risk of relapsing into depression after stopping antidepressants is high, but no established predictors exist. Resting-state functional magnetic resonance imaging (rsfMRI) measures may help predict relapse and identify the mechanisms by which relapses occur. rsfMRI data were acquired from healthy controls and from patients with remitted major depressive disorder on antidepressants. Patients were assessed a second time either before or after discontinuation of the antidepressant, and followed up for six months to assess relapse. A seed-based functional connectivity analysis was conducted focusing on the left subgenual anterior cingulate cortex and left posterior cingulate cortex. Seeds in the amygdala and dorsolateral prefrontal cortex were explored. 44 healthy controls (age: 33.8 (10.5), 73% female) and 84 patients (age: 34.23 (10.8), 80% female) were included in the analysis. 29 patients went on to relapse and 38 remained well. The seed-based analysis showed that discontinuation resulted in an increased functional connectivity between the right dorsolateral prefrontal cortex and the parietal cortex in non-relapsers. In an exploratory analysis, this functional connectivity predicted relapse risk with a balanced accuracy of 0.86. Further seed-based analyses, however, failed to reveal differences in functional connectivity between patients and controls, between relapsers and non-relapsers before discontinuation and changes due to discontinuation independent of relapse. In conclusion, changes in the connectivity between the dorsolateral prefrontal cortex and the posterior default mode network were associated with and predictive of relapse after open-label antidepressant discontinuation. This finding requires replication in a larger dataset.
Application of feed forward and recurrent neural networks in simulation of left ventricular mechanics
Authors: Dabiri Yaghoub , Van der Velden Alex , Sack Kevin L. , Choy Jenny S. , Guccione Julius M. , Kassab Ghassan S. 
Published: December 2020

AbstractAn understanding of left ventricle (LV) mechanics is fundamental for designing better preventive, diagnostic, and treatment strategies for improved heart function. Because of the costs of clinical and experimental studies to treat and understand heart function, respectively, in-silico models play an important role. Finite element (FE) models, which have been used to create in-silico LV models for different cardiac health and disease conditions, as well as cardiac device design, are time-consuming and require powerful computational resources, which limits their use when real-time results are needed. As an alternative, we sought to use deep learning (DL) for LV in-silico modeling. We used 80 four-chamber heart FE models for feed forward, as well as recurrent neural network (RNN) with long short-term memory (LSTM) models for LV pressure and volume. We used 120 LV-only FE models for training LV stress predictions. The active material properties of the myocardium and time were features for the LV pressure and volume training, and passive material properties and element centroid coordinates were features of the LV stress prediction models. For six test FE models, the DL error for LV volume was 1.599 ± 1.227 ml, and the error for pressure was 1.257 ± 0.488 mmHg; for 20 LV FE test examples, the mean absolute errors were, respectively, 0.179 ± 0.050 for myofiber, 0.049 ± 0.017 for cross-fiber, and 0.039 ± 0.011 kPa for shear stress. After training, the DL runtime was in the order of seconds whereas equivalent FE runtime was in the order of several hours (pressure and volume) or 20 min (stress). We conclude that using DL, LV in-silico simulations can be provided for applications requiring real-time results.
Solid-phase extraction cartridges with multi-walled carbon nanotubes and effect of the oxygen functionalities on the recovery efficiency of organic micropollutants
Authors: Barbosa Marta O. , Ribeiro Rui S. , Ribeiro Ana R. L. , Pereira M. Fernando R. , Silva Adrián M. T. 
Published: December 2020

AbstractPristine and functionalized multi-walled carbon nanotubes (MWCNTs) were investigated as adsorbent materials inside solid-phase extraction (SPE) cartridges for extraction and preconcentration of 8 EU-relevant organic micropollutants (with different pKa and polarity) before chromatographic analysis of surface water. The recoveries obtained were > 60% for 5/8 target pollutants (acetamiprid, atrazine, carbamazepine, diclofenac, and isoproturon) using a low amount of this reusable adsorbent (50 mg) and an eco-friendly solvent (ethanol) for both conditioning and elution steps. The introduction of oxygenated surface groups in the carbon nanotubes by using a controlled HNO3 hydrothermal oxidation method, considerably improved the recoveries obtained for PFOS (perfluorooctanesulfonic acid) and methiocarb, which was ascribed to the hydrogen bond adsorption mechanism, but decreased those observed for the pesticide acetamiprid and for two pharmaceuticals (carbamazepine and diclofenac), suggesting π–π dispersive interactions. Moreover, a good correlation was found between the recovery obtained for methiocarb and the amount of oxygenated surface groups on functionalized MWCNTs, which was mainly attributed to the increase of phenols and carbonyl and quinone groups. Thus, the HNO3 hydrothermal oxidation method can be used to finely tune the surface chemistry (and texture) of MWCNTs according to the specific micropollutants to be extracted and quantified in real water samples.
Evaluation of product of two sigmoidal membership functions (psigmf) as an ANFIS membership function for prediction of nanofluid temperature
Authors: Babanezhad Meisam , Nakhjiri Ali Taghvaie , Marjani Azam , Rezakazemi Mashallah , Shirazian Saeed 
Published: December 2020

AbstractA nanofluid containing water and nanoparticles made of copper (Cu) inside a cavity with square shape is simulated utilizing the computational fluid dynamics (CFD) approach. The nanoparticles made up 15% of the nanofluid. By performing the simulation, the CFD output is characterized by the coordinates in the x, y, nanofluid temperature, and velocity in the y-direction that these outputs are obtained for different physical time iterations. Moreover, the CFD outputs are examined by one of the artificial techniques, i.e. adaptive network-based fuzzy inference system (ANFIS). For this purpose, the data was clustered via grid partition clustering, and the type of membership functions (MFs) was chosen product of two sigmoidal membership functions (psigmf). After reaching 99.9% of intelligence in ANFIS, the nanofluid temperature is predicted for the entire data, which are included in the learning processes. The results showed that the method of ANFIS can predict the thermal properties in different physical times at different computing points without having a training background at those times. Additionally, this study shows that with three membership functions at each input, the model’s accuracy is higher than four functions.
Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon
Authors: Makkay Andrea M. , Louyakis Artemis S. , Ram-Mohan Nikhil , Gophna Uri , Gogarten J. Peter , Papke R. Thane 
Published: December 2020

AbstractHorizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeonHaloferax volcaniiinvolves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating inHfx. volcanii.
Transcriptional profiles of human islet and exocrine endothelial cells in subjects with or without impaired glucose metabolism
Authors: Jonsson Alexander , Hedin Anders , Müller Malin , Skog Oskar , Korsgren Olle 
Published: December 2020

AbstractIn experimental studies, pancreatic islet microvasculature is essential for islet endocrine function and mass, and islet vascular morphology is altered in diabetic subjects. Even so, almost no information is available concerning human islet microvascular endothelial cell (MVEC) physiology and gene expression. In this study, islets and exocrine pancreatic tissue were acquired from organ donors with normoglycemia or impaired glucose metabolism (IGM) immediately after islet isolation. Following single-cell dissociation, primary islet- and exocrine MVECs were obtained through fluorescence-activated cell sorting (FACS) and transcriptional profiles were generated using AmpliSeq. Multiple gene sets involved in general vascular development and extracellular matrix remodeling were enriched in islet MVEC. In exocrine MVEC samples, multiple enriched gene sets that relate to biosynthesis and biomolecule catabolism were found. No statistically significant enrichment was found in gene sets related to autophagy or endoplasmic reticulum (ER) stress. Although ample differences were found between islet- and exocrine tissue endothelial cells, no differences could be observed between normoglycemic donors and donors with IGM at gene or gene set level. Our data is consistent with active angiogenesis and vascular remodeling in human islets and support the notion of ongoing endocrine pancreas tissue repair and regeneration even in the adult human.