bluuebunny/crossref_metadata_2025_split huggingface dataset:
TrimNet: learning molecular representation from triplet messages for biomedicine
Authors: Li Pengyong , Li Yuquan , Hsieh Chang-Yu , Zhang Shengyu , Liu Xianggen , Liu Huanxiang , Song Sen , Yao Xiaojun 
Published: October 2020

AbstractMotivationComputational methods accelerate drug discovery and play an important role in biomedicine, such as molecular property prediction and compound–protein interaction (CPI) identification. A key challenge is to learn useful molecular representation. In the early years, molecular properties are mainly calculated by quantum mechanics or predicted by traditional machine learning methods, which requires expert knowledge and is often labor-intensive. Nowadays, graph neural networks have received significant attention because of the powerful ability to learn representation from graph data. Nevertheless, current graph-based methods have some limitations that need to be addressed, such as large-scale parameters and insufficient bond information extraction.ResultsIn this study, we proposed a graph-based approach and employed a novel triplet message mechanism to learn molecular representation efficiently, named triplet message networks (TrimNet). We show that TrimNet can accurately complete multiple molecular representation learning tasks with significant parameter reduction, including the quantum properties, bioactivity, physiology and CPI prediction. In the experiments, TrimNet outperforms the previous state-of-the-art method by a significant margin on various datasets. Besides the few parameters and high prediction accuracy, TrimNet could focus on the atoms essential to the target properties, providing a clear interpretation of the prediction tasks. These advantages have established TrimNet as a powerful and useful computational tool in solving the challenging problem of molecular representation learning.AvailabilityThe quantum and drug datasets are available on the website of MoleculeNet: http://moleculenet.ai. The source code is available in GitHub: https://github.com/yvquanli/trimnet.Contactxjyao@lzu.edu.cn, songsen@tsinghua.edu.cn
EWASex: an efficient R-package to predict sex in epigenome-wide association studies
Authors: Lund Jesper Beltoft , Li Weilong , Mohammadnejad Afsaneh , Li Shuxia , Baumbach Jan , Tan Qihua 
Published: October 2020

Abstract

Summary
Epigenome-Wide Association Study (EWAS) has become a powerful approach to identify epigenetic variations associated with diseases or health traits. Sex is an important variable to include in EWAS to ensure unbiased data processing and statistical analysis. We introduce the R-package EWASex, which allows for fast and highly accurate sex-estimation using DNA methylation data on a small set of CpG sites located on the X-chromosome under stable X-chromosome inactivation in females.

Results
We demonstrate that EWASex outperforms the current state of the art tools by using different EWAS datasets. With EWASex, we offer an efficient way to predict and to verify sex that can be easily implemented in any EWAS using blood samples or even other tissue types. It comes with pre-trained weights to work without prior sex labels and without requiring access to RAW data, which is a necessity for all currently available methods.

Availability and implementation
The EWASex R-package along with tutorials, documentation and source code are available at https://github.com/Silver-Hawk/EWASex.

Supplementary information
Supplementary data are available at Bioinformatics online.
Detection of crossover points in detrended fluctuation analysis: an application to EEG signals of patients with epilepsy
Authors: Mesquita Victor Barreto , Oliveira Filho Florêncio Mendes , Rodrigues Paulo Canas 
Published: October 2020

Abstract

Motivation
The quantification of long-range correlation of electroencephalogram (EEG) signals is an important research direction for its relevance in helping understanding the brain activity. Epileptic seizures have been studied in the past years where different non-linear statistical approaches have been employed to understand the relationship between the EEG signal and the epileptic discharge. One of the most widely used method for to analyse long memory processes is the detrended fluctuation analysis (DFA). However, no objective and pragmatic methods have been developed to detect crossover points and reference channels in DFA.

Results
In this article, we propose: (i) two automatic approaches that successfully detect crossover points in DFA related methods on the log–log plot and (ii) a criteria to choose the reference channel for the log-amplitude function. Moreover, the DFA is applied to EEG signals of 10 epileptic patients collected from the CHB-MIT database, being the log-amplitude function used to compare the different brain hemispheres by making use of the methodology proposed in the article. The existence of long-range power-law correlations is demonstrated and indicates that the EEG signals of epileptic patients present three well-defined regions with the first region showing a 1/f noise (pink noise) for seven subjects and a random walk behaviour for three subjects. The second and third regions show anti-persistence behaviour. Moreover, the results of the log-amplitude function were divided in two groups: the first, including seven subjects, where the increase in the scales results in an increase in the fluctuation in the frontal channels and the second, included three subjects, where the fluctuation for large scales are greater for the parietal channels.

Availability and implementation
The functions used in this article are available in the R package DFA (Mesquita et al., 2020).

Supplementary information
Supplementary data are available at Bioinformatics online.
CYP46A1-dependent and independent effects of efavirenz treatment
Authors: Mast Natalia , El-Darzi Nicole , Petrov Alexey M , Li Young , Pikuleva Irina A 
Published: October 2020

AbstractCholesterol excess in the brain is mainly disposed via cholesterol 24-hydroxylation catalysed by cytochrome P450 46A1, a CNS-specific enzyme. Cytochrome P450 46A1 is emerging as a promising therapeutic target for various brain diseases with both enzyme activation and inhibition having therapeutic potential. The rate of cholesterol 24-hydroxylation determines the rate of brain cholesterol turnover and the rate of sterol flux through the plasma membranes. The latter was shown to affect membrane properties and thereby membrane proteins and membrane-dependent processes. Previously we found that treatment of 5XFAD mice, an Alzheimer’s disease model, with a small dose of anti-HIV drug efavirenz allosterically activated cytochrome P450 46A1 in the brain and mitigated several disease manifestations. Herein, we generated Cyp46a1−/−5XFAD mice and treated them, along with 5XFAD animals, with efavirenz to ascertain cytochrome P450 46A1-dependent and independent drug effects. Efavirenz-treated versus control Cyp46a1−/−5XFAD and 5XFAD mice were compared for the brain sterol and steroid hormone content, amyloid β burden, protein and mRNA expression as well as synaptic ultrastructure. We found that the cytochrome P450 46A1-dependent efavirenz effects included changes in the levels of brain sterols, steroid hormones, and such proteins as glial fibrillary acidic protein, Iba1, Munc13-1, post-synaptic density-95, gephyrin, synaptophysin and synapsin-1. Changes in the expression of genes involved in neuroprotection, neurogenesis, synaptic function, inflammation, oxidative stress and apoptosis were also cytochrome P450 46A1-dependent. The total amyloid β load was the same in all groups of animals, except lack of cytochrome P450 46A1 decreased the production of the amyloid β40 species independent of treatment. In contrast, altered transcription of genes from cholinergic, monoaminergic, and peptidergic neurotransmission, steroid sulfation and production as well as vitamin D3 activation was the main CYP46A1-independent efavirenz effect. Collectively, the data obtained reveal that CYP46A1 controls cholesterol availability for the production of steroid hormones in the brain and the levels of biologically active neurosteroids. In addition, cytochrome P450 46A1 activity also seems to affect the levels of post-synaptic density-95, the main postsynaptic density protein, possibly by altering the calcium/calmodulin-dependent protein kinase II inhibitor 1 expression and activity of glycogen synthase kinase 3β. Even at a small dose, efavirenz likely acts as a transcriptional regulator, yet this regulation may not necessarily lead to functional effects. This study further confirmed that cytochrome P450 46A1 is a key enzyme for cholesterol homeostasis in the brain and that the therapeutic efavirenz effects on 5XFAD mice are likely realized via cytochrome P450 46A1 activation.
Compromised thermal tolerance of cardiovascular capacity in upstream migrating Arctic char and brown trout—are hot summers threatening migrating salmonids?
Authors: Mottola Giovanna , Kristensen Torstein , Anttila Katja 
Published: October 2020

AbstractHeat waves are threatening fish around the world, leading sometimes to mass mortality events. One crucial function of fish failing in high temperatures is oxygen delivery capacity, i.e. cardiovascular function. For anadromous salmonids, increased temperature could be especially detrimental during upstream migration since they need efficiently working oxygen delivery system in order to cross the river rapids to reach upstream areas. The migration also occurs during summer and early autumn exposing salmonids to peak water temperatures, and in shallow rivers there is little availability for thermal refuges as compared to thermally stratified coastal and lake habitats. In order to shed light on the mechanisms underpinning the capacity of migrating fish to face high environmental temperatures, we applied a physiological and molecular approach measuring cardiovascular capacities of migrating and resident Arctic char (Salvelinus alpinus) and brown trout (Salmo trutta) in Northern Norway. The maximum cardiovascular capacity of migrating fish was significantly lower compared to the resident conspecifics. The onset of cardiac impairment started only 2°C higher than river temperature, meaning that even a small increase in water temperature may already compromise cardiac function. The migrating fish were also under significant cellular stress, expressing increased level of cardiac heat shock proteins. We consider these findings highly valuable when addressing climate change effect on migrating fish and encourage taking action in riverine habitat conservation policies. The significant differences in upper thermal tolerance of resident and migrating fish could also lead changes in population dynamics, which should be taken into account in future conservation plans.
The role of CD36 in cardiovascular disease
Authors: Shu Hongyang , Peng Yizhong , Hang Weijian , Nie Jiali , Zhou Ning , Wang Dao Wen 
Published: October 2020

Abstract
CD36, also known as the scavenger receptor B2, is a multifunctional receptor widely expressed in various organs. CD36 plays a crucial role in the uptake of long-chain fatty acids, the main metabolic substrate in myocardial tissue. The maturation and transportation of CD36 is regulated by post-translational modifications, including phosphorylation, ubiquitination, glycosylation, and palmitoylation. CD36 is decreased in pathological cardiac hypertrophy caused by ischaemia–reperfusion and pressure overload, and increased in diabetic cardiomyopathy and atherosclerosis. Deficiency of CD36 alleviates diabetic cardiomyopathy and atherosclerosis, while overexpression of CD36 eliminates ischaemia–reperfusion damage, together suggesting that CD36 is closely associated with the progression of cardiovascular diseases and may be a new therapeutic target. This review summarizes the regulation and post-translational modifications of CD36 and evaluates its role in cardiovascular diseases and its potential as a therapeutic target.
Effects of Parasitoid Age, Host Egg Age, and Host Egg Freezing on Reproductive Success of Ooencyrtus mirus (Hymenoptera: Encyrtidae) on Bagrada hilaris (Hemiptera: Pentatomidae) Eggs
Authors: Power Nancy , Ganjisaffar Fatemeh , Xu Karen , Perring Thomas M 
Published: October 2020

Abstract
Bagrada hilaris (Burmeister) is a serious pest on brassica crops in many regions throughout the world. As part of our efforts to enhance biological control, we have been studying an egg parasitoid that was collected from B. hilaris eggs found on brassica plant debris in Pakistan. This species has recently been described as Ooencyrtus mirus Triapitsyn & Power. A major component of rearing biological control agents is understanding the relationship among host egg age, parasitoid age, and reproductive success. To this end, we used a factorial design to evaluate all combinations of host egg ages 0–5 d and parasitoid ages 0–11 d. The results showed that the best combinations are 0- to 1-d-old host eggs with 3- to 10-d-old parasitoids. A further study using frozen host eggs showed that O. mirus can reproduce as successfully on frozen B. hilaris eggs as on fresh ones.
Cardiac amyloidosis mimicking acute coronary syndrome: a case report and literature review
Authors: Nguyen Huan T , Nguyen Chuyen T H 
Published: October 2020

AbstractBackgroundCardiac amyloidosis, a progressive cardiac disease, results from the accumulation of undegraded proteinaceous substrates in the extracellular matrix of the heart. It may present as acute coronary syndrome (ACS); therefore, a clear distinction remains challenging in clinical practice. We describe a case of cardiac amyloidosis mimicking ACS.Case summaryA 72-year-old man experienced chest discomfort for 2 days. He gradually developed dyspnoea during the preceding month. Electrocardiogram (ECG) showed sinus rhythm with right bundle branch block and low voltage. Echocardiography revealed concentric left ventricular thickening, biatrial dilation, and preserved ejection fraction with predominantly left ventricular basal hypokinesis. Serial testing of the cardiac biomarkers showed persistently increased high-sensitive cardiac troponin T levels and normal serum creatine kinase myocardial band levels. He was diagnosed with ACS with haemodynamic stability. However, coronary angiography demonstrated non-obstructive coronary arteries. Furthermore, significant macroglossia and periorbital purpura were noticed. Laboratory investigations revealed elevated serum immunoglobulin free light chain (FLC) kappa and lambda levels with an increased FLC ratio. Histological analysis of the biopsied abdominal skin confirmed amyloidosis.DiscussionCardiac amyloidosis often presents as restrictive cardiomyopathy. The usual symptoms include dyspnoea and peripheral oedema. Chest pain may manifest rarely, leading to misdiagnosis as coronary artery disease. Some findings suggestive of cardiac amyloidosis include clinical signs such as amyloid deposits, dyspnoea, low ECG voltage, and basal-predominant hypokinesis with relative apical sparing in echocardiography. Serum FLC test and abdominal skin biopsy can confirm the diagnosis of amyloidosis when a myocardial biopsy is not feasible.
Perceptions of co-designing health promotion interventions with Indigenous communities in New Zealand
Authors: Harding Truely , Oetzel John G , Foote Jeff , Hepi Maria 
Published: October 2020

Summary
Health inequities among Indigenous and non-Indigenous communities are well documented and the research literature includes robust discussions about innovative ways to reduce inequities including co-design. Co-designing health promotion interventions with Indigenous communities presents many benefits and challenges for researchers, health professionals and communities involved in the process. The purpose of this study was to identify the facilitators and barriers of co-designing a health promotion intervention with Māori communities. Additionally, this study considers a specific Māori co-design framework, He Pikinga Waiora (HPW). HPW is a participatory approach to creating interventions emphasizing community engagement, systems thinking and centred on Kaupapa Māori (an approach grounded in Māori worldviews). The research design for this study was Kaupapa Māori. Participants (n = 19) in this study were stakeholders in the New Zealand health sector. Participants were interviewed using an in-depth, semi-structured protocol. Thematic analysis was employed to analyse the data. Facilitators for co-designing health promotion interventions with Māori communities were collaboration and community voice. Barriers identified were mismanaged expectations and research constraints. Finally, facilitators for the HPW framework included providing clear guidelines and being grounded in Māori perspectives, while barriers included limited concrete case studies, jargon and questions about sustainability. Collaboration and inclusion of community voice supports the development of more effective co-design health promotion interventions within Māori communities which may address health inequities. The HPW framework offers clear guidelines and Māori perspectives which may assist in the development of effective co-design health promotion interventions, although areas for improvement were suggested.
Alogliptin Attenuates Lipopolysaccharide-Induced Neuroinflammation in Mice Through Modulation of TLR4/MYD88/NF-κB and miRNA-155/SOCS-1 Signaling Pathways
Authors: El-Sahar Ayman E , Shiha Nesma A , El Sayed Nesrine S , Ahmed Lamiaa A 
Published: October 2020

Abstract

Background
Endotoxin-induced neuroinflammation plays a crucial role in the pathogenesis and progression of various neurodegenerative diseases. A growing body of evidence supports that incretin-acting drugs possess various neuroprotective effects that can improve learning and memory impairments in Alzheimer’s disease models. Thus, the present study aimed to investigate whether alogliptin, a dipeptidyl peptidase-4 inhibitor, has neuroprotective effects against lipopolysaccharide (LPS)-induced neuroinflammation and cognitive impairment in mice as well as the potential mechanisms underlying these effects.

Methods
Mice were treated with alogliptin (20 mg/kg/d; p.o.) for 14 days, starting 1 day prior to intracerebroventricular LPS injection (8 μg/μL in 3 μL).

Results
Alogliptin treatment alleviated LPS-induced cognitive impairment as assessed by Morris water maze and novel object recognition tests. Moreover, alogliptin reversed LPS-induced increases in toll-like receptor 4 and myeloid differentiation primary response 88 protein expression, nuclear factor-κB p65 content, and microRNA-155 gene expression. It also rescued LPS-induced decreases in suppressor of cytokine signaling gene expression, cyclic adenosine monophosphate (cAMP) content, and phosphorylated cAMP response element binding protein expression in the brain.

Conclusion
The present study sheds light on the potential neuroprotective effects of alogliptin against intracerebroventricular LPS-induced neuroinflammation and its associated memory impairment via inhibition of toll-like receptor 4/ myeloid differentiation primary response 88/ nuclear factor-κB signaling, modulation of microRNA-155/suppressor of cytokine signaling-1 expression, and enhancement of cAMP/phosphorylated cAMP response element binding protein signaling.
Exploratory Shopping: Attention Affects In-Store Exploration and Unplanned Purchasing
Authors: Streicher Mathias C , Estes Zachary , Büttner Oliver B 
Published: October 2020

Abstract
A fundamental function of retailing is to bring products into the view of shoppers, because viewing products can activate forgotten or new needs. Retailers thus employ various strategies to entice shoppers to explore the product assortment and store environment, in the hopes of stimulating unplanned purchasing. This article investigates consumers’ breadth of attention as a mechanism of such in-store exploration and hence of unplanned purchasing. Specifically, attentional breadth is the focus that is directed to a wider or more limited area in processing visual scenes. Across several lab and field experiments, the authors show that shoppers’ attentional breadth activates an exploratory mindset that stimulates visual and physical exploration of shopping environments, ultimately affecting their product choices and unplanned purchasing. The results also show that more impulsive buyers are more susceptible to these effects. The present article thus complements and constrains prior theorizing on mindset theory, attention, store exploration, and unplanned purchasing, all of which are of practical importance to both retailers and consumers.
Modeling the Turbulent Wake Behind a Wall-Mounted Square Cylinder
Authors: Amor Christian , Pérez José M , Schlatter Philipp , Vinuesa Ricardo , Le Clainche Soledad 
Published: October 2020

Abstract
This article introduces some soft computing methods generally used for data analysis and flow pattern detection in fluid dynamics. These techniques decompose the original flow field as an expansion of modes, which can be either orthogonal in time (variants of dynamic mode decomposition), or in space (variants of proper orthogonal decomposition) or in time and space (spectral proper orthogonal decomposition), or they can simply be selected using some sophisticated statistical techniques (empirical mode decomposition). The performance of these methods is tested in the turbulent wake of a wall-mounted square cylinder. This highly complex flow is suitable to show the ability of the aforementioned methods to reduce the degrees of freedom of the original data by only retaining the large scales in the flow. The main result is a reduced-order model of the original flow case, based on a low number of modes. A deep discussion is carried out about how to choose the most computationally efficient method to obtain suitable reduced-order models of the flow. The techniques introduced in this article are data-driven methods that could be applied to model any type of non-linear dynamical system, including numerical and experimental databases.
Simulations of the merging galaxy cluster Abell 2034: what determines the level of separation between gas and dark matter
Authors: Moura Micheli T , Machado Rubens E G , Monteiro-Oliveira Rogério 
Published: October 2020

ABSTRACT
Cluster mergers are an important laboratory for studying the behaviour of dark matter (DM) and intracluster gas. There are dissociative collisions that can separate the intracluster gas from the DM. Abell 2034 presents clear dissociative features observed by X-rays and gravitational lensing. The cluster, at z = 0.114, consists of two substructures with mass ratio of about 1:2.2, separated by ∼720 kpc. The X-ray emission peak is offcentred from the south DM peak by ∼350 kpc. Using N-body hydrodynamical simulations, we aim to reconstruct the dynamic history of the collision, reproducing the observed features, and also to explore the conditions that led to the dissociation. Our best model assuming that the collision is close to the plane of the sky, with a small impact parameter, observed 0.26 Gyr after central passage, reproduces the observed features of this cluster, such as the offset between X-ray and DM peaks, X-ray morphology, and temperatures. We explored several variations using different gas and DM concentrations for each cluster. The level of dissociation was quantified by the distances between X-ray and DM peaks, and also by the gas retention in the cluster cores. We found that the ratio of central gas densities is more important than the ratio of central DM densities in determining the level of dissociation.