bluuebunny/crossref_metadata_2025 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

Motivation

Computational 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.

Results

In 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.

Availability

The 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.

Contact

xjyao@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

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

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

Cholesterol 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

Heat 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.
Social Workers as School Administrators: A New Approach to the U.S. Public Education System
Authors: Lige Kathryn
Published: October 2020

The education system is a key contributor in preparing children to be future leaders in society, yet current educational standards have failed to adequately address mental health and social justice issues that students face. School leadership positions have historically been reserved for seasoned teachers; however, with the proper training and certifications, social workers may be equipped to lead schools beyond providing social services. U.S. public K–12 education leaders across the nation are recognizing that students’ needs are best understood by looking to their social environment, which has been a major principal in the field of social work for decades. Therefore, hiring social workers as school administrators is a considerable option to cultivate improved academic and social–emotional outcomes through school- and districtwide leadership.
The role of CD36 in cardiovascular disease
Authors: Shu Hongyang , Peng Yizhong , Hang Weijian , Nie Jiali , Zhou Ning , Wang Dao Wen
Published: October 2020

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

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

Background

Cardiac 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 summary

A 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.

Discussion

Cardiac 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

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

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

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

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.
Wrongful Conviction in Sexual Assault
Authors: Johnson Matthew Barry
Published: October 2020

Wrongful Conviction in Sexual Assault: Stranger Rape, Acquaintance Rape, and Intra-Familial Child Sexual Assaults examines the phenomenon of innocent defendants who are convicted of rape and related sexual offenses. It presents findings that indicate sexual offenses are highly overrepresented among confirmed wrongful convictions. Drawing from Innocence Project and National Registry of Exoneration data and supplemented by social science and historical sources, the investigation explores various processes that led to wrongful conviction, distinguishing the differential risk of wrongful conviction among stranger rape, acquaintance rape, and intra-familial child sexual assault. The book includes reference to established research on false confessions, eyewitness misidentification, erroneous expert and informant testimony, DNA evidence, racial bias, and “manufactured” evidence. The work also introduces new terms and concepts (such as “black box” investigation methods, the stranger rape thesis, the moral outrage–moral correction process, “spontaneous misidentification,” victim status paths, the differential investigation challenge related to capable vs. incapacitated rape victims, and the role of serial sexual offending in wrongful conviction) to clarify and illustrate unique aspects of wrongful conviction in sexual assault.
Race and Rape Prosecution in US History
Authors: Johnson Matthew Barry
Published: October 2020

This chapter examines the current disproportion of Black defendants wrongly convicted of sexual assault through a historical lens. It notes the US history of statutorily separate sexual assault penalties based on race of the defendant and victim. Throughout US history the legal definition and societal response to rape (and rape allegations) have been influenced by considerations of race. These considerations were consistently made to the detriment of Black defendants charged with rape. The chapter reviews how race, rape law, and prosecution have been manifested in different historical eras (the period of race-based enslavement, the period of Jim Crow segregation, and the current post–civil rights period) and the mechanisms of racial bias against Black defendants in the post–civil rights era.
Trauma and Sexual Objectification of Women with Serious Mental Illness
Authors: Mizock Lauren , Carr Erika
Published: October 2020

This chapter reviews the feminist framework of objectification theory to help providers understand the unique experiences of women who live in a culture that views and values their bodies as sexual objects. The literature related to sexual objectification is explored, as well as the empirical links to mental health problems. The literature on sexual exploitation of women who experience serious mental illness is also examined. The implications of these unique intersecting experiences of women with serious mental illness are discussed. This chapter includes two case narratives, a clinical strategies list, discussion questions, activities, and a clinical worksheet (“Gender Role Analysis Worksheet”).
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

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.
The Evolution of Gas-Phase Metallicity and Resolved Abundances in Star-forming Galaxies at z ≈ 0.6 – 1.8
Authors: Gillman S , Tiley A L , Swinbank A M , Dudzevičiūtė U , Sharples R M , Smail Ian , Harrison C M , Bunker Andrew J , Bureau Martin , Cirasuolo M , Magdis Georgios E , Mendel Trevor , Stott John P
Published: October 2020

We present an analysis of the chemical abundance properties of ≈650 star-forming galaxies at z ≈ 0.6 – 1.8. Using integral-field observations from the K - band Multi-Object Spectrograph (KMOS), we quantify the [N ii]/Hα emission-line ratio, a proxy for the gas-phase Oxygen abundance within the interstellar medium. We define the stellar mass – metallicity relation at z ≈ 0.6 – 1.0 and z ≈ 1.2 – 1.8 and analyse the correlation between the scatter in the relation and fundamental galaxy properties (e.g. Hα star-formation rate, Hα specific star-formation rate, rotation dominance, stellar continuum half-light radius and Hubble-type morphology). We find that for a given stellar mass, more highly star-forming, larger and irregular galaxies have lower gas-phase metallicities, which may be attributable to their lower surface mass densities and the higher gas fractions of irregular systems. We measure the radial dependence of gas-phase metallicity in the galaxies, establishing a median, beam smearing-corrected, metallicity gradient of ΔZ/ΔR= 0.002 ± 0.004 dex kpc−1, indicating on average there is no significant dependence on radius. The metallicity gradient of a galaxy is independent of its rest-frame optical morphology, whilst correlating with its stellar mass and specific star-formation rate, in agreement with an inside-out model of galaxy evolution, as well as its rotation dominance. We quantify the evolution of metallicity gradients, comparing the distribution of ΔZ/ΔR in our sample with numerical simulations and observations at z ≈ 0 – 3. Galaxies in our sample exhibit flatter metallicity gradients than local star-forming galaxies, in agreement with numerical models in which stellar feedback plays a crucial role redistributing metals.
The distribution of neutral hydrogen in the colour–magnitude plane of galaxies
Authors: Dutta Saili , Khandai Nishikanta
Published: October 2020

We present the conditional H i (neutral hydrogen) mass function (HIMF) conditioned on observed optical properties, Mr (r-band absolute magnitude), and Cur (u − r colour), for a sample of 7709 galaxies from Arecibo Legacy Fast ALFA (40 per cent data release – α.40) which overlaps with a common volume in SDSS DR7. Based on the conditional HIMF, we find that the luminous red, luminous blue, and faint blue populations dominate the total HIMF at the high-mass end, knee, and the low-mass end, respectively. We use the conditional HIMF to derive the underlying distribution function of ΩH i (H i density parameter), p(ΩH i), in the colour–magnitude plane of galaxies. The distribution, p(ΩH i), peaks in the blue cloud at $\mathit{ M_{{r}}}^{\text{max}}=-19.25, \mathit{ C_{{ur}}}^{\text{max}}=1.44$ but is skewed. It has a long tail towards faint blue galaxies, and luminous red galaxies. We argue that p(ΩH i) can be used to reveal the underlying relation between cold gas, stellar mass, and the star formation rate in an unbiased way, that is, the derived relation does not suffer from survey or sample selection.
The deubiquitinase USP36 Regulates DNA replication stress and confers therapeutic resistance through PrimPol stabilization
Authors: Yan Yuanliang , Xu Zhijie , Huang Jinzhou , Guo Guijie , Gao Ming , Kim Wootae , Zeng Xiangyu , Kloeber Jake A , Zhu Qian , Zhao Fei , Luo Kuntian , Lou Zhenkun
Published: October 2020

PrimPol has been recently identified as a DNA damage tolerant polymerase that plays an important role in replication stress response. However, the regulatory mechanisms of PrimPol are not well defined. In this study, we identify that the deubiquitinase USP36 interferes with degradation of PrimPol to regulate the replication stress response. Mechanistically, USP36 is deubiquitinated following DNA replication stress, which in turn facilitates its upregulation and interaction with PrimPol. USP36 deubiquitinates K29-linked polyubiquitination of PrimPol and increases its protein stability. Depletion of USP36 results in replication stress-related defects and elevates cell sensitivity to DNA-damage agents, such as cisplatin and olaparib. Moreover, USP36 expression positively correlates with the level of PrimPol protein and poor prognosis in patient samples. These findings indicate that the regulation of PrimPol K29-linked ubiquitination by USP36 plays a critical role in DNA replication stress and chemotherapy response.
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API
Authors: Mi Huaiyu , Ebert Dustin , Muruganujan Anushya , Mills Caitlin , Albou Laurent-Philippe , Mushayamaha Tremayne , Thomas Paul D
Published: October 2020

PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all domains of life. The evolutionary classification is based on a library of over 15,000 phylogenetic trees, and the functional classifications include Gene Ontology terms and pathways. Here, we analyze the current coverage of genes from genomes in different taxonomic groups, so that users can better understand what to expect when analyzing a gene list using PANTHER tools. We also describe extensive improvements to PANTHER made in the past two years. The PANTHER Protein Class ontology has been completely refactored, and 6101 PANTHER families have been manually assigned to a Protein Class, providing a high level classification of protein families and their genes. Users can access the TreeGrafter tool to add their own protein sequences to the reference phylogenetic trees in PANTHER, to infer evolutionary context as well as fine-grained annotations. We have added human enhancer-gene links that associate non-coding regions with the annotated human genes in PANTHER. We have also expanded the available services for programmatic access to PANTHER tools and data via application programming interfaces (APIs). Other improvements include additional plant genomes and an updated PANTHER GO-slim.
Trade-off analysis of agri-food systems for sustainable research and development
Authors: Antle John M , Valdivia Roberto O
Published: October 2020

Tradeoff Analysis (TOA) is an approach to positive analysis that combines foresight analysis and simulation modeling tools from the relevant disciplines, including economics, in a participatory process designed to formulate and evaluate forward-looking, strategic decisions under high levels of uncertainty in complex systems. We motivate TOA with a prototype framework for the design and evaluation of public-good agricultural research for sustainable development. We discuss the advantages of TOA over conventional economic analysis-Benefit-Cost Analysis-for the design and evaluation of sustainable development pathways. The remainder of the paper describes the currently available modeling tools and their strengths and limitations for use in TOA, and illustrates recent applications with cross-scale case studies. We conclude with a discussion of the opportunities and challenges for the use of foresight analysis and TOA in research priority setting and management at global and project levels, using the case of the CGIAR to illustrate.
The effect of consumers’ supermarket competence on information search and shopping outcomes in two Balkan cities
Authors: Grunert Klaus G , Haas Rainer , Imami Drini , Miftari Iliriana
Published: October 2020

Distribution systems for food can change quickly in emergent markets, requiring new competences for consumers, and even in some European countries we have seen considerable changes in the distribution system for food in recent decades, raising the question whether consumers have acquired corresponding competences. We take two Balkan countries, Albania and Kosovo, as a case in point and measure consumers’ competence in dealing with package and price information in supermarkets and how this affects their information search behavior and the outcome of their shopping trips in terms of shopping pleasure, shopping trip satisfaction, and perceived risk. Results from data collected in the two countries’ main cities, Pristina and Tirana, show that higher levels of competence lead to more information search and better shopping outcomes, but that information search in certain cases can also increase perceived risk and diminish pleasure and satisfaction. In addition, considerable differences in the two cities can be found, which can be linked to differences in their history.
“Positive discrimination doesn’t mean anything”: Understanding Black French Ambivalence toward Affirmative Action
Authors: Fleming Crystal M , Girma Hewan
Published: October 2020

Using in-depth qualitative interviews with French Caribbeans of African descent (N=52) in the Paris region, this study examines minority perspectives on the possibility of racial or ethnic affirmative action in France. Through a narrative analysis of their justifications for supporting or criticizing affirmative action, we find that the majority of our respondents expressed reservations over the possibility of quotas and other affirmative action initiatives, with many describing ambivalent views and mixed emotions. In explaining their discomfort with the idea and implementation of affirmative action, respondents point to concerns over the efficacy and legitimacy of such policies, a moral defense of meritocracy, and their own reluctance to admit the failures of French Republicanism. Critics of affirmative action combine race-conscious and colorblind discourse, expressing both a challenge to colorblind notions of universalism and a nostalgic appeal to its rhetoric. With regard to migration status, we find that members of the second-generation express more ambivalent views, while members of the first generation are more emphatic in their opposition. Finally, we argue for greater attention to the dynamics of racial ambivalence in the study of anti-racism and affirmative action.
Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000–18
Authors: Han Zhenzhi , Song Yang , Xiao Jinbo , Jiang Lili , Huang Wei , Wei Haiyan , Li Jie , Zeng Hanri , Yu Qiuli , Li Jiameng , Yu Deshan , Zhang Yanjun , Li Chonghai , Zhan Zhifei , Shi Yonglin , Xiong Ying , Wang Xianjun , Ji Tianjiao , Yang Qian , Zhu Shuangli , Yan Dongmei , Xu Wenbo , Zhang Yong
Published: October 2020

Hand, foot, and mouth disease (HFMD), which is a frequently reported and concerning disease worldwide, is a severe burden on societies globally, especially in the countries of East and Southeast Asia. Coxsackievirus A16 (CV-A16) is one of the most important causes of HFMD and a severe threat to human health, especially in children under 5 years of age. To investigate the epidemiological characteristics, spread dynamics, recombinant forms (RFs), and other features of CV-A16, we leveraged the continuous surveillance data of CV-A16-related HFMD cases collected over an 18-year period. With the advent of the EV-A71 vaccine since 2016, which targeted the EV-A71-related HFMD cases, EV-A71-related HFMD cases decreased dramatically, whereas the CV-A16-related HFMD cases showed an upward trend from 2017 to October 2019. The CV-A16 strains observed in this study were genetically related and widely distributed in the mainland of China. Our results show that three clusters (B1a–B1c) existed in the mainland of China and that the cluster of B1b dominates the diffusion of CV-A16 in China. We found that eastern China played a decisive role in seeding the diffusion of CV-A16 in China, with a more complex and variant transmission trend. Although EV-A71 vaccine was launched in China in 2016, it did not affect the genetic diversity of CV-A16, and its genetic diversity did not decline, which confirmed the epidemiological surveillance trend of CV-A16. Two discontinuous clusters (2000–13 and 2014–18) were observed in the full-length genome and arranged along the time gradient, which revealed the reason why the relative genetic diversity of CV-A16 increased and experienced more complex fluctuation model after 2014. In addition, the switch from RFs B (RF-B) and RF-C co-circulation to RF-D contributes to the prevalence of B1b cluster in China after 2008. The correlation between genotype and RFs partially explained the current prevalence of B1b. This study provides unprecedented full-length genomic sequences of CV-A16 in China, with a wider geographic distribution and a long-term time scale. The study presents valuable information about CV-A16, aimed at developing effective control strategies, as well as a call for a more robust surveillance system, especially in the Asia-Pacific region.
Role of Body Cast Application for Scoliosis Associated With Prader-Willi Syndrome
Authors: van Bosse Harold J.P.
Published: October 2020

Background:

Prader-Willi syndrome (PWS) is a rare genetic syndrome, with a prevalence of infantile scoliosis of ~23%. These curves are likely related to severe hypotonia. Approximately 15% of children with PWS will need surgical intervention for their scoliosis. The purpose of this study was to evaluate the effectiveness of curing or controlling moderate and severe infantile scoliosis curves in children with PWS.

Methods:

This single institution, retrospective study of patients with PWS and infantile scoliosis reviewed 34 consecutive children with >24 months follow-up from initiation of serial spinal casting. Cobb angle comparison measurements of radiographs taken precasting, during treatment, and at follow-up were performed. Rib-vertebral angle difference, Nash-Moe rotation, and space available for lung measurements were followed. Outcomes were stratified as “Cured,” “Braced,” and “Surgery.”

Results:

Average age for first cast for the entire study was 32 months (range, 14 to 64), undergoing 8 casts (range, 3 to 18) over 25 months (range, 9 to 57) for an initial curve of 54 degrees (range, 27 to 106 degrees), which improved to 27 degrees (range, 11 to 78 degrees). In total, 12 patients (35%) were in the Cured group, following 6 casts over 17 months, with an initial curve of 44±14 degrees improving to 17±5 degrees at the end of treatment, and 20±18 degrees at 68-month follow-up. In total, 18 patients were in the Braced group, with curves initially improving from 55±14 degrees to 35±14 degrees, but at 47±20 degrees at 51-month follow-up. Four patients needed surgery, with initial curves 85 degrees (range, 54 to 106 degrees), but surgery could be postponed 56 months (range, 40 to 73) by casting. Rib-vertebral angle difference was not prognostic.

Conclusions:

Serial spinal casting is effective in for treating infantile scoliosis in children with PWS. One third of patients had their curve resolved, at least temporarily, where they were braced and cast free. The others were able to delay surgery for a number of years. Initial curves <50 degrees in children <3 years of age seem to have the best prognosis.

Level of Evidence:

Level IV.
A Novel Small Deletion in the ATP2A2 Gene in a Patient with Sporadic Darier's Disease and Concomitant Depression: A Case Report
Authors: Wang Chong , Luan Jing , Niu Zhen-Min , Huang Qiong , Zhang Zheng-Hua
Published: October 2020

Introduction:

Darier's disease is a rare autosomal dominant skin disorder caused by mutations in ATP2A2. Recently, the high prevalence of neuropsychiatric symptoms is frequently reported in Darier's disease patients.

We present a case of patient with concurrence of Darier's disease and depression and detected the mutations in ATP2A2.

Case presentation:

A 29-year-old man presented with a 15-year history of brown, harsh keratotic papules on his scalp, face, neck, trunk, axilla, ingunia and upper limbs. Meanwhile, he had persistent depression. He was diagnosed as Darier's disease according to clinical manifestations and result of histological examination. We sequenced all coding regions of ATP2A2. The mutation c.2993_2994del (p. Val998Alafs∗33) in exon 20 of ATP2A2 was detected.

Discussion:

Darier's disease has been associated with several extracutaneous manifestations, in particular neuropsychiatric morbidity. Likely gene disrupting mutations in ATP2A2 was reported to have a close relationship to Darier's disease cases with reported co-occurring neuropsychiatric features. Consistent with the previous reports, an likely gene disrupting mutations was detected in our patient with concurrence of DD and depression.

Conclusion:

The psychiatric disorders in patients with Darier's disease should be well appreciated .The underlying mechanism in correlation between the mutation in ATP2A2 and neuropsychiatric phenotypes in Darier's disease remain unclarified and warrants further investigation.
Sex-Related Differences in the Risk of Silicosis Among Chinese Pottery Workers
Authors: Poinen-Rughooputh Satiavani , Rughooputh Mahesh Shumsher , Guo Yanjun , Lai Hanpeng , Sun Weiwei , Chen Weihong
Published: October 2020

Objectives:

To investigate the effect of sex on the risk of silicosis and to explore any interaction between cigarette smoking and sex in the development of silicosis.

Methods:

The cohort was selected from eight Chinese pottery factories. Diagnoses of silicosis were based on 1986 Chinese pneumoconiosis Roentgen diagnostic criteria. Data on cigarette smoking were collected by face-to-face interviews in 1989 and 2003.

Results:

Eight thousand eight hundred and eighty seven dust-exposed workers were included. Men had a 77% higher incidence of silicosis than women. At lower pack-years of smoking, men were 72% more at risk than women. The latency period was found to be longest in female never-smokers and shortest in female ever-smokers.

Conclusions:

Men had a higher risk of developing silicosis than women. Cigarette smoking increased the risk in both sexes, more so in women.
Exoscope-assisted Otologic Surgery During the COVID-19 Pandemic
Authors: Tu Nathan , Bojrab Dennis , Sioshansi Pedrom , Lin Kenny , Hong Robert , Bojrab Dennis , Babu Seilesh
Published: October 2020

Objective:

The recent COVID-19 pandemic has required careful reconsideration of safe operating room practices. We describe our initial experiences performing otologic surgery with the exoscope during the COVID-19 pandemic.

Method:

The exoscope was used for several semiurgent otologic surgeries in combination with complete eye protection, a “tent” drape, a smoke evacuator with ultra-low particulate air filter, and betadine irrigation. These techniques are demonstrated in the accompanying video. This was compared with our experiences using the microscope.

Results:

The described modified goggles allowed complete eye protection while providing a fully three-dimensional view of the surgical site. The other safety measures described are simple and efficient techniques which can easily be adopted for otologic surgery using the microscope.

Conclusion:

Use of the exoscope for otologic surgery during the COVID-19 pandemic allows full three-dimensional visualization of the surgical field while simultaneously providing complete eye protection. Use of the “tent” drape, ultra-low particulate air filter, and betadine irrigation are also options that otologic surgeons may consider for additional safety.