bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co‐oxidation of Antarctic krill oil with whey protein and myofibrillar protein in oil‐in‐water emulsions
Authors: Wang Yuliu , Liu Yanzi , Ma Lei , Yang Lu , Cong Peixu , Lan Haohui , Xue Changhu , Xu Jie 
Published: October 2020

AbstractAntarctic krill oil (AKO) is usually encapsulated by the protein materials, enhancing its oxidative stability. Proteins exhibit immense effect on lipid oxidation and induce protein–lipid co‐oxidation. This study aimed at elucidating the co‐oxidation mechanism of AKO and whey protein (WP) or myofibrillar protein (MP) in oil‐in‐water emulsions. The estimations of malondialdehyde (MDA) content, phospholipid molecular species, and pyrrole content resulted in increased and decreased oxidation rate of AKO (especially phosphatidylethanolamine) by WP and MP, respectively. Meanwhile, protein concentration, sulfhydryl content, the loss of tryptophan fluorescence intensity, and sodium dodecyl sulfate‐polyacrylamide gel electrophoresis results demonstrated that AKO promoted WP oxidation but inhibited MP oxidation. Further, the antioxidative abilities of seven common antioxidants were evaluated. Ascorbyl palmitate showed the most substantial antioxidative effect for both AKO and proteins (about 70% decrease of MDA content and 30% decrease of the decrease ratio of tryptophan fluorescence intensity). This finding supported that different proteins could exhibit different pro/anti‐oxidative effects on lipid oxidation, especially for marine lipids abundant in phospholipids and polyunsaturated fatty acids. Besides, MP could also act as antioxidant in MP AKO emulsions, further extending its application from traditional surfactants.Practical ApplicationAKO is usually encapsulated by the protein materials, enhancing its oxidative stability. The results demonstrated MP could inhibit AKO oxidation, and vice versa, especially when ascorbyl palmitate was added at the same time. As a result, this finding explored a new potential wall material with antioxidative ability for the encapsulated products of AKO.
Biomolecular composition of capping layer and stability of biogenic selenium nanoparticles synthesized by five bacterial species
Authors: Bulgarini Alessandra , Lampis Silvia , Turner Raymond J. , Vallini Giovanni 
Published: October 2020

SummaryBiogenic metal/metalloid nanoparticles of microbial origin retain a functional biomolecular capping layer that confers structural stability. Little is known about the composition of such capping material. In this study, selenium nanoparticles (SeNPs) synthesized by five different bacterial strains underwent comparative analysis with newly proposed protocols for quantifying the concentration of carbohydrates, proteins and lipids present in capping layers. SeNPs were therefore treated with two different detergents to remove portions of the surrounding caps in order to assess the resulting effects. Capping material quantification was carried out along with the measure of parameters such as hydrodynamic diameter, polydispersity and surface charge. SeNPs from the five strains showed differences in their distinct biomolecule ratios. On the other hand, structural changes in the nanoparticles induced by detergents did not correlate with the amounts of capping matrix removed. Thus, the present investigation suggests a hypothesis to describe capping layer composition of the bacterial SeNPs: some biomolecules are bound more strongly than others to the core metalloid matrix, so that the diverse capping layer components differentially contribute to the overall structural characteristics of the nanoparticles. Furthermore, the application of the approach here in combining quantification of cap‐associated biomolecules with the measurement of structural integrity‐related parameters can give the biogenic nanomaterial field useful information to construct a data bank on biogenically synthesized nanostructures.
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML
Authors: Edler Daniel , Klein Johannes , Antonelli Alexandre , Silvestro Daniele 
Published: October 2020

Abstract

raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood.

Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front‐end to setup and run phylogenetic analyses.

Our program offers automated pipelines for analyses that require multiple successive calls of RAxML, built‐in functions to concatenate alignment files while automatically specifying the appropriate partition settings, and one‐click model testing to select the best substitution models using ModelTest‐NG. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML‐NG, which provides new functionality and higher performance on large datasets.

raxmlGUI 2.0 facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.
Hierarchical computing for hierarchical models in ecology
Authors: McCaslin Hanna M. , Feuka Abigail B. , Hooten Mevin B. 
Published: October 2020

Abstract

Bayesian hierarchical models allow ecologists to account for uncertainty and make inference at multiple scales. However, hierarchical models are often computationally intensive to fit, especially with large datasets, and researchers face trade‐offs between capturing ecological complexity in statistical models and implementing these models.

We present a recursive Bayesian computing (RB) method that can be used to fit Bayesian models efficiently in sequential MCMC stages to ease computation and streamline hierarchical inference. We also introduce transformation‐assisted RB (TARB) to create unsupervised MCMC algorithms and improve interpretability of parameters. We demonstrate TARB by fitting a hierarchical animal movement model to obtain inference about individual‐ and population‐level migratory characteristics.

Our recursive procedure reduced computation time for fitting our hierarchical movement model by half compared to fitting the model with a single MCMC algorithm. We obtained the same inference fitting our model using TARB as we obtained fitting the model with a single algorithm.

For complex ecological statistical models, like those for animal movement, multi‐species systems, or large spatial and temporal scales, the computational demands of fitting models with conventional computing techniques can limit model specification, thus hindering scientific discovery. Transformation‐assisted RB is one of the most accessible methods for reducing these limitations, enabling us to implement new statistical models and advance our understanding of complex ecological phenomena.
Targeting miR‐124/Ferroportin signaling ameliorated neuronal cell death through inhibiting apoptosis and ferroptosis in aged intracerebral hemorrhage murine model
Authors: Bao Wen‐Dai , Zhou Xiao‐Ting , Zhou Lan‐Ting , Wang Fudi , Yin Xiaoping , Lu Youming , Zhu Ling‐Qiang , Liu Dan 
Published: October 2020

AbstractIncidence of intracerebral hemorrhage (ICH) and brain iron accumulation increases with age. Excess iron accumulation in brain tissues post‐ICH induces oxidative stress and neuronal damage. However, the mechanisms underlying iron deregulation in ICH, especially in the aged ICH model have not been well elucidated. Ferroportin1 (Fpn) is the only identified nonheme iron exporter in mammals to date. In our study, we reported that Fpn was significantly upregulated in perihematomal brain tissues of both aged ICH patients and mouse model. Fpn deficiency induced by injecting an adeno‐associated virus (AAV) overexpressing cre recombinase into aged Fpn‐floxed mice significantly worsened the symptoms post‐ICH, including hematoma volume, cell apoptosis, iron accumulation, and neurologic dysfunction. Meanwhile, aged mice pretreated with a virus overexpressing Fpn showed significant improvement of these symptoms. Additionally, based on prediction of website tools, expression level of potential miRNAs in ICH tissues and results of luciferase reporter assays, miR‐124 was identified to regulate Fpn expression post‐ICH. Higher serum miR‐124 levels were correlated with poor neurologic scores of aged ICH patients. Administration of miR‐124 antagomir enhanced Fpn expression and attenuated iron accumulation in aged mice model. Both apoptosis and ferroptosis, but not necroptosis, were regulated by miR‐124/Fpn signaling manipulation. Our study demonstrated the critical role of miR‐124/Fpn signaling in iron metabolism and neuronal death post‐ICH in aged murine model. Thus, Fpn upregulation or miR‐124 inhibition might be promising therapeutic approachs for this disease.
Sulforaphane prevents age‐associated cardiac and muscular dysfunction through Nrf2 signaling
Authors: Bose Chhanda , Alves Ines , Singh Preeti , Palade Philip T. , Carvalho Eugenia , Børsheim Elisabet , Jun Se‐Ran , Cheema Amrita , Boerma Marjan , Awasthi Sanjay , Singh Sharda P. 
Published: October 2020

AbstractAge‐associated mitochondrial dysfunction and oxidative damage are primary causes for multiple health problems including sarcopenia and cardiovascular disease (CVD). Though the role of Nrf2, a transcription factor that regulates cytoprotective gene expression, in myopathy remains poorly defined, it has shown beneficial properties in both sarcopenia and CVD. Sulforaphane (SFN), a natural compound Nrf2‐related activator of cytoprotective genes, provides protection in several disease states including CVD and is in various stages of clinical trials, from cancer prevention to reducing insulin resistance. This study aimed to determine whether SFN may prevent age‐related loss of function in the heart and skeletal muscle. Cohorts of 2‐month‐old and 21‐ to 22‐month‐old mice were administered regular rodent diet or diet supplemented with SFN for 12 weeks. At the completion of the study, skeletal muscle and heart function, mitochondrial function, and Nrf2 activity were measured. Our studies revealed a significant drop in Nrf2 activity and mitochondrial functions, together with a loss of skeletal muscle and cardiac function in the old control mice compared to the younger age group. In the old mice, SFN restored Nrf2 activity, mitochondrial function, cardiac function, exercise capacity, glucose tolerance, and activation/differentiation of skeletal muscle satellite cells. Our results suggest that the age‐associated decline in Nrf2 signaling activity and the associated mitochondrial dysfunction might be implicated in the development of age‐related disease processes. Therefore, the restoration of Nrf2 activity and endogenous cytoprotective mechanisms by SFN may be a safe and effective strategy to protect against muscle and heart dysfunction due to aging.
Assessing the Role of Long Noncoding RNA in Nucleus Accumbens in Subjects With Alcohol Dependence
Authors: Drake John , McMichael Gowon O. , Vornholt Eric Sean , Cresswell Kellen , Williamson Vernell , Chatzinakos Chris , Mamdani Mohammed , Hariharan Siddharth , Kendler Kenneth S. , Kalsi Gursharan , Riley Brien P. , Dozmorov Mikhail , Miles Michael F. , Bacanu Silviu‐Alin , Vladimirov Vladimir I. 
Published: October 2020

BackgroundLong noncoding RNA (lncRNA) have been implicated in the etiology of alcohol use. Since lncRNA provide another layer of complexity to the transcriptome, assessing their expression in the brain is the first critical step toward understanding lncRNA functions in alcohol use and addiction. Thus, we sought to profile lncRNA expression in the nucleus accumbens (NAc) in a large postmortem alcohol brain sample.MethodsLncRNA and protein‐coding gene (PCG) expressions in the NAc from 41 subjects with alcohol dependence (AD) and 41 controls were assessed via a regression model. Weighted gene coexpression network analysis was used to identify lncRNA and PCG networks (i.e., modules) significantly correlated with AD. Within the significant modules, key network genes (i.e., hubs) were also identified. The lncRNA and PCG hubs were correlated via Pearson correlations to elucidate the potential biological functions of lncRNA. The lncRNA and PCG hubs were further integrated with GWAS data to identify expression quantitative trait loci (eQTL).ResultsAt Bonferroni adj. p‐value ≤ 0.05, we identified 19 lncRNA and 5 PCG significant modules, which were enriched for neuronal and immune‐related processes. In these modules, we further identified 86 and 315 PCG and lncRNA hubs, respectively. At false discovery rate (FDR) of 10%, the correlation analyses between the lncRNA and PCG hubs revealed 3,125 positive and 1,860 negative correlations. Integration of hubs with genotype data identified 243 eQTLs affecting the expression of 39 and 204 PCG and lncRNA hubs, respectively.ConclusionsOur study identified lncRNA and gene networks significantly associated with AD in the NAc, coordinated lncRNA and mRNA coexpression changes, highlighting potentially regulatory functions for the lncRNA, and our genetic (cis‐eQTL) analysis provides novel insights into the etiological mechanisms of AD.
Red Blood Cell Distribution Width as a Predictor of 28‐Day Mortality in Critically Ill Patients With Alcohol Use Disorder
Authors: Liao Lin , Pinhu Liao 
Published: October 2020

BackgroundPatients with alcohol use disorder (AUD) are common attendees of the intensive care unit (ICU). Early assessment of the prognosis for critically ill patients with AUD is conducive for formulating comprehensive treatment measures and improving survival rates. The purpose of this study was to explore the predictive value of red blood cell distribution width (RDW) for 28‐day mortality in critically ill patients with AUD.Methods2,884 patients with AUD were recruited retrospectively. Data from the MIMIC‐III database were collected and analyzed. A receiver operating characteristic (ROC) curve was used to determine the optimal cutoff value of RDW. The Kaplan–Meier method and Cox regression models were used to evaluate prognostic factors.ResultsOf the 2,884 patients, there were 344 nonsurvivors (11.9%). The nonsurvivors had a higher RDW than the survivors (p < 0.001). According to ROC curve analysis, the area under the curve predicted by RDW for 28‐day mortality was 0.728 (95% CI, 0.700 to 0.755) and the optimal cutoff value was 15.45% (sensitivity: 67.2%; specificity: 67.3%). Length of stay in ICU, length of stay in hospital, in‐hospital mortality, and 28‐day mortality in patients with an RDW > 15.45% were significantly higher than in those with an RDW ≤ 15.45% (p < 0.001). Cox regression analysis showed that an RDW > 15.45% was an independent prognostic indicator for 28‐day mortality in critically ill patients with AUD (HR = 1.964, 95% CI: 1.429 to 2.698).ConclusionsHigh RDW was associated with increased short‐term mortality risks in critically ill patients with AUD.
The Effect of Chronic Ethanol Exposure and Thiamine Deficiency on Myelin‐related Genes in the Cortex and the Cerebellum
Authors: Chatterton Bradley J. , Nunes Polliana T. , Savage Lisa M. 
Published: October 2020

BackgroundLong‐term alcohol consumption has been linked to structural and functional brain abnormalities. Furthermore, with persistent exposure to ethanol (EtOH), nutrient deficiencies often develop. Thiamine deficiency is a key contributor to alcohol‐related brain damage and is suspected to contribute to white matter pathology. The expression of genes encoding myelin proteins in several cortical brain regions is altered with EtOH exposure. However, there is limited research regarding the impact of thiamine deficiency on myelin dysfunction.MethodsA rat model was used to assess the impact of moderate chronic EtOH exposure (CET; 20% EtOH in drinking water for 1 or 6 months), pyrithiamine‐induced thiamine deficiency treatment (PTD), both conditions combined (CET‐PTD), or CET with thiamine injections (CET + T) on myelin‐related gene expression (Olig1, Olig2, MBP, MAG, and MOG) in the frontal and parietal cortices and the cerebellum.ResultsThe CET‐PTD treatments caused the greatest suppression in myelin‐related genes in the cortex. Specifically, the parietal cortex was the region that was most susceptible to PTD‐CET‐induced alterations in myelin‐related genes. In addition, PTD treatment, with and without CET, caused minor fluctuations in the expression of several myelin‐related genes in the frontal cortex. In contrast, CET alone and PTD alone suppressed several myelin‐related genes in the cerebellum. Regardless of the region, there was significant recovery of myelin‐related genes with extended abstinence and/or thiamine restoration.ConclusionModerate chronic EtOH alone had a minor effect on the suppression of myelin‐related genes in the cortex; however, when combined with thiamine deficiency, the reduction was amplified. There was a suppression of myelin‐related genes following long‐term EtOH and thiamine deficiency in the cerebellum. However, the suppression in the myelin‐related genes mostly occurred 24 h after EtOH removal or following thiamine restoration; within 3 weeks of abstinence or thiamine recovery, gene expression rebounded.
Changes in Circulating Metabolome Precede Alcohol‐Related Diseases in Middle‐Aged Men: A Prospective Population‐Based Study With a 30‐Year Follow‐Up
Authors: Kärkkäinen Olli , Klåvus Anton , Voutilainen Ari , Virtanen Jyrki , Lehtonen Marko , Auriola Seppo , Kauhanen Jussi , Rysä Jaana 
Published: October 2020

BackgroundHeavy alcohol use has been associated with altered circulating metabolome. We investigated whether changes in the circulating metabolome precede incident diagnoses of alcohol‐related diseases.MethodsThis is a prospective population‐based cohort study where the participants were 42‐ to 60‐year‐old males at baseline (years 1984 to 1989). Subjects who received a diagnosis for an alcohol‐related disease during the follow‐up were defined as cases (n = 92, mean follow‐up of 13.6 years before diagnosis). Diagnoses were obtained through linkage with national health registries. We used 2 control groups: controls who self‐reported similar levels of alcohol use as compared to cases at baseline (alcohol‐controls, n = 92), and controls who self‐reported only light drinking at baseline (control‐controls, n = 90). A nontargeted metabolomics analysis of baseline serum samples was performed.ResultsThere were significant differences between the study groups in the baseline serum levels of 64 metabolites: in amino acids (e.g., glutamine [FDR‐corrected q‐value = 0.0012]), glycerophospholipids (e.g., lysophosphatidylcholine 16:1 [q = 0.0008]), steroids (e.g., cortisone [q = 0.00001]), and fatty acids (e.g., palmitoleic acid [q = 0.0031]). The main finding was that after controlling for baseline levels of self‐reported alcohol use and the biomarker of alcohol use, gamma‐glutamyl transferase, and when compared to both alcohol‐control and control‐control group, the alcohol‐case group had lower serum levels of asparagine (Cohen’s d = −0.48 [95% CI −0.78 to −0.19] and d = −0.49 [−0.78 to −0.19], respectively) and serotonin (d = −0.45 [−0.74 to −0.15], and d = −0.46 [−0.75 to −0.16], respectively), with no difference between the two control groups (asparagine d = 0.00 [−0.29 to 0.29] and serotonin d = −0.01 [−0.30 to 0.29]).ConclusionsChanges in the circulating metabolome, especially lower serum levels of asparagine and serotonin, are associated with later diagnoses of alcohol‐related diseases, even after adjustment for the baseline level of alcohol use.
Changes in Drinking Contexts over the Night Course: Concurrent and Lagged Associations with Adolescents’ Nightly Alcohol Use
Authors: Finan Laura J. , Lipperman‐Kreda Sharon 
Published: October 2020

BackgroundExamining underage drinking contexts can advance the field of adolescent substance use prevention by supporting and informing interventions that can target adolescents in specific contexts. The current study examines how concurrent and lagged situational (i.e., alcohol availability and adult supervision), social (i.e., the number of people and presence of friends), and location (i.e., home vs other location) context characteristics change risks for alcohol use over the night course.MethodsText messages with links to online surveys were used to collect ecological momentary assessment (EMA) data over 2 weekends from adolescents in California. Data were collected using adolescents’ personal cell phones early and late in the evening and the following morning. Analyses were limited to adolescents with at least 1 drinking occasion during EMA (N = 58; Mage = 16.64, SD = 0.74; 48% female; 83% White).ResultsDrinking earlier in the evening was positively associated with continued drinking over the night course. Context characteristics were found to play important concurrent and lagged roles in increasing the likelihood of alcohol use over evening hours.ConclusionsFindings indicated substantive concurrent and lagged social, situational, and location‐based contextual effects on adolescent alcohol use over the course of an evening. Importantly, context characteristics were differentially associated with alcohol use over the course of the evening. The fact that these contextual factors are modifiable suggests that the use of prevention strategies delivered to adolescents throughout the evening may reduce adolescents’ drinking and related problems over the evening hours.
Evaluating the effectiveness of the smartphone app, Drink Less, compared with the NHS alcohol advice webpage, for the reduction of alcohol consumption among hazardous and harmful adult drinkers in the UK at 6‐month follow‐up: protocol for a randomised controlled trial
Authors: Garnett Claire , Oldham Melissa , Angus Colin , Beard Emma , Burton Robyn , Field Matt , Greaves Felix , Hickman Matthew , Kaner Eileen , Loebenberg Gemma , Michie Susan , Munafò Marcus , Pizzo Elena , Brown Jamie 
Published: October 2020

ABSTRACTBackground and AimsDigital interventions are effective for reducing alcohol consumption but evidence is limited regarding smartphone apps. Drink Less is a theory‐ and evidence‐informed app to help people reduce their alcohol consumption that has been refined in terms of its content and design for usability across the sociodemographic spectrum. We aim to evaluate the effectiveness and cost‐effectiveness of recommending Drink Less at reducing alcohol consumption compared with usual digital care.DesignTwo‐arm individually randomised controlled trial.SettingOnline trial in the United Kingdom (UK).ParticipantsHazardous or harmful drinkers (Alcohol Use Disorders Identification Test [AUDIT] score ≥8) aged 18+ who want to drink less alcohol (n = 5562). Participants will be recruited from July 2020 to May 2022 using multiple strategies with a focus on remote digital methods.Intervention and comparatorParticipants will be randomised to receive either an email recommending that they use Drink Less (intervention) or view the National Health Service (NHS) webpage on alcohol advice (comparator).MeasurementsThe primary outcome is change in self‐reported weekly alcohol consumption, assessed using the extended AUDIT‐Consumption, between baseline and 6‐month follow‐up. Secondary outcomes include change in self‐reported weekly alcohol consumption assessed at 1‐ and 3‐month follow‐ups, and the proportion of hazardous drinkers; alcohol‐related problems and injury; health‐related quality of life; and use of health services assessed at 6‐month follow‐up. Effectiveness will be examined with adjusted regression models, adjusting for baseline alcohol consumption and using an intention‐to‐treat approach. A mixed‐methods process evaluation will assess engagement, acceptability and mechanism of action. Economic evaluations will be conducted using both a short‐ and longer‐term time horizon.CommentsThis study will establish the effectiveness and cost‐effectiveness of the Drink Less app at reducing alcohol consumption among hazardous and harmful adult drinkers and will be the first randomised controlled trial of an alcohol reduction app for the general population in the United Kingdom. This study will inform the decision on whether it is worth investing resources in large‐scale implementation.