bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct activation of zebrafish neurons by ultrasonic stimulation revealed by whole CNS calcium imaging
Authors: Meneghetti N , Dedola F , Gavryusev V , Sancataldo G , Turrini L , de Vito G , Tiso N , Vanzi F , Carpaneto J , Cutrone A , Pavone F Saverio , Micera S , Mazzoni A
Published: August 2020

Objective. Ultrasounds (US) use in neural engineering is so far mainly limited to ablation through high intensity focused ultrasound, but interesting preliminary results show that low intensity low frequency ultrasound could be used instead to modulate neural activity. However, the extent of this modulatory ability of US is still unclear, as in in vivo studies it is hard to disentangle the contribution to neural responses of direct activation of the neuron by US stimulation and indirect activation due either to sensory response to mechanical stimulation associated to US, or to propagation of activity from neighboring areas. Here, we aim to show how to separate the three effects and assess the presence of direct response to US stimulation in zebrafish. Approach. We observed in zebrafish larvae brain-wide US-induced activity patterns through calcium imaging microscopy. Sensory response to mechanical stimulation was assessed with a US shield. Activity propagation was assessed with inter-area latency evaluation. Main results. We prove that in selected brain regions the zebrafish’s neural response is mainly due to direct activation, later spreading to the other regions. Shielding the neurons from direct US stimulation resulted in a significantly attenuated response, showing that sensory stimulation does not play a prominent role. Significance. US non-invasive neuromodulatory approach might lead to novel ways to test and control neural activity, and hence to novel neuromodulatory therapies. Future studies will focus on the biophysical structure of directly responsive neurons to capture the mechanisms of US induced activity.
The health impacts of waste-to-energy emissions: a systematic review of the literature
Authors: Cole-Hunter Tom , Johnston Fay H , Marks Guy B , Morawska Lidia , Morgan Geoffrey G , Overs Marge , Porta-Cubas Ana , Cowie Christine T
Published: August 2020

Waste-to-energy (WtE) processes, or the combustion of refuse-derived fuel (RDF) for energy generation, has the potential to reduce landfill volume while providing a renewable energy source. We aimed to systematically review and summarise current evidence on the potential health effects (benefits and risks) of exposure to WtE/RDF-related combustion emissions.

We searched PubMed and Google Scholar using terms related to health and WtE/RDF combustion emissions, following PRISMA guidelines. Two authors independently screened titles, abstracts and then full-texts of original, peer-reviewed research articles published until 20th March 2020, plus their relevant references. Overall quality of included epidemiological studies were rated using an amended Navigation framework.

We found 19 articles from 269 search results that met our inclusion criteria, including two epidemiological studies, five environmental monitoring studies, seven health impact or risk assessments (HIA/HRA), and five life-cycle assessments. We found a dearth of health studies related to the impacts of exposure to WtE emissions. The limited evidence suggests that well-designed and operated WtE facilities using sorted feedstock (RDF) are critical to reduce potential adverse health (cancer and non-cancer) impacts, due to lower hazardous combustion-related emissions, compared to landfill or unsorted incineration. Poorly fed WtE facilities may emit concentrated toxins with serious potential health risks, such as dioxins/furans and heavy metals; these toxins may remain problematic in bottom ash as a combustion by-product. Most modelling studies estimate that electricity (per unit) generated from WtE generally emits less health-relevant air pollutants (also less greenhouse gases) than from combustion of fossil fuels (e.g. coal). Some modelled estimates vary due to model sensitivity for type of waste processed, model inputs used, and facility operational conditions.

We conclude that rigorous assessment (e.g. HRA including sensitivity analyses) of WtE facility/technological characteristics and refuse type used is necessary when planning/proposing facilities to protect human health as the technology is adopted worldwide.
High performance exhaled breath biomarkers for diagnosis of lung cancer and potential biomarkers for classification of lung cancer
Authors: Long Yijing , Wang Chunyan , Wang Tianzhi , Li Wenwen , Dai Wei , Xie Shaohua , Tian Yonghui , Liu Mingxin , Liu Yifeng , Peng Xiaoqin , Liu Yuanling , Zhang Yinchenxi , Wang Ruxin , Li Qiang , Duan Yixiang
Published: August 2020

Exhaled breath analysis has emerged as a promising non-invasive method for diagnosing lung cancer (LC), whereas reliable biomarkers are lacking. Herein, a standardized and systematic study was presented for LC diagnosis, classification and metabolism exploration. To improve the reliability of biomarkers, a validation group was included, and quality control for breath sampling and analysis, comprehensive pollutants analysis, and strict biomarker screening were performed. The performance of exhaled breath biomarkers was shown to be excellent in diagnosing LC even in early stages (stage I and II) with surpassing 0.930 area under the receiver operating characteristic (ROC) curve (AUC), 90% of sensitivity and 88% of specificity both in the discovery and validation analyses. Meanwhile, in these two groups, diagnosing subtypes of LC attained AUCs over 0.930 and reached 1.00 in the two subtypes of adenocarcinomas. It is demonstrated that the metabolism changes in LC are possibly related to lipid oxidation, gut microbial, cytochrome P450 and glutathione S-transferase, and glutathione pathways change in LC progression. Overall, the reliable biomarkers contribute to the clinical application of breath analysis in screening LC patients as well as those in early stages.
Low-carbon economic dispatching model of electric-heating combined system considering multi-type energy storage
Authors: Pan Xiao , Liang Yi , Deng Xinyang , Li Minchao , Cui Jia , Yang Junyou
Published: August 2020

In order to reduce the wind abandonment rate during the winter heating period in the “Three North” region and the environmental pollution caused by carbon emissions during power generation, this paper proposes a low-carbon economic dispatching model that takes into account multiple types of energy storage for electric-heating combined systems. First, a multi-type energy storage model with electric boilers, electric energy storage, and heat storage as the core is proposed, and its internal energy conversion, storage, and output links are refined. Then, a carbon trading mechanism is introduced into electric heating. The combined system, taking into account the cost of carbon trading, and aiming at the lowest overall operating cost of the system, construct a low-carbon economic dispatching model for wind-power, conventional thermal power units, combined heat and power units, and multiple types of energy-storage combined heat and power systems. Yalmip/Gurobi solved the model and analysed the wind power consumption effect and carbon emission situation in the dispatching mode through numerical simulation. Simulation results show that under carbon trading, participation of multiple types of energy storage can effectively improve wind power utilization and the economic and environmental benefits of the system.
Research on the business model of power retail market under the energy Internet
Authors: Li Yongbo , Qian Hanhan , Liu Dunnan , Li Genzhu
Published: August 2020

With the continuous development of the energy Internet, small and micro market entities are given the right to choose independently. Multiple new entities such as distributed energy, virtual power plants, electric vehicles, interactive energy use enter the power market and participate in power trading, creating an open and shared power market environment. At the same time, with the deepening of China’s power system reform, the focus of market construction will shift from wholesale side to retail side. Therefore, it is urgent to study the business model of power retail market, so as to take necessary preventive measures and avoidance measures as early as possible to avoid and reduce the pressure and risk faced by grid companies.
Feasibility study of typhoon disaster economic loss assessment based on random forest
Authors: Wang Fei
Published: August 2020

Based on the disaster-causing factors and the actual disaster-causing factors of typhoon disasters, this paper selects 9 assessment indicators, obtains an effective sample set through noise processing, and uses a random forest algorithm to set up a typhoon disaster economic loss assessment model. The model verification and results show that the random forest model has very obvious advantages in both single-level evaluation accuracy and total evaluation accuracy, and can meet the consistency with the actual evaluation standards. The GINI index reduction value obtained through model feedback can be used as an indicator of importance, and the indicator of the number of disaster victims is the most important factor of economic loss.
Correlation study on environmental performance of Chengdu and economic development
Authors: Wei Wei , Shang Yingnan , Zhou Xiaoying , Wen Bo , Wang Jiecai , Jiang Yijing , Li Zuocheng
Published: August 2020

This paper evaluated the environmental performance from 2013 to 2018 based on establishing environmental performance assessment system of Chengdu and the correlation of environmental performance increasing rate and GDP increasing rate was analyzed. In addition, Pearson’s correlation analysis on environmental performance index and GDP was carried out by using SPSS and we can see from the results that environmental performance shows an increasing tendency with the growth of GDP, environmental performance increasing rate is lower than GDP increasing rate. And there was no obvious correlation between environmental performance index and GDP (some high economical areas have low environmental performance levels). In another word, the rapid development of the economy does little help to rapidly improve environmental performance level. So Chengdu should pay more attention to protect environment, and be a coordinated development relationship between economy and environment.
Field investigation on rural domestic sewage discharge in a typical village of the Taihu Lake Basin
Authors: Xu Yuye , Lu Xiwu , Chen Fangkui
Published: August 2020

Rural sewage is an important non-point pollution that aggravates eutrophication of the Taihu Lake. Practically grasping the characteristics of local villages’ sewage treatment demand, sewage flow and sewage quality has far-reaching significance for constructing suitable and efficient rural sewage treatment systems, and ultimately improving the water environment of the lake basin. To this end, the study conducted a field investigation in a typical village of the Taihu Lake Basin in July and continuously monitored sewage flow and sewage quality in the mode of sewage classification. The sewage quality test included chemical oxygen demand (COD), total nitrogen (TN), ammonia nitrogen (NH3-N), and total phosphorus (TP). This paper reviewed the development status of the typical village and demonstrated the rules of rural domestic water consumption and sewage discharge. It was found that the total sewage discharge flow in summer was around 88.90 L/(cap . d) and the hourly variation coefficient was around 3.92. Kitchen sewage, washing sewage, and toilet sewage had significant differences in sewage quality. Particularly, the nitrogen and phosphorus nutrients in toilet sewage were quite rich, accounting for 84.42% and 61.90% of the corresponding total load, respectively. Thus, the ideas of properties-classified treatment and resource treatment were worth being introduced into the rural sewage treatment process.
Analysis of chlorinated hydrocarbon source of groundwater in the eastern part of a city
Authors: Liu Shusen , Ma Zhenmin , Zhang Shuaiji
Published: August 2020

In order to control the pollution of chlorinated hydrocarbons in groundwater, it is necessary to analyze the source of chlorinated hydrocarbons in groundwater. Therefore, this paper uses the method of factor analysis and multiple linear regression equation to analyze the source of the study area. The results show that the pollution sources in the study area can be summarized as chemical enterprise pollution sources, electromechanical manufacturing pollution sources, chemical fiber pollution sources and pesticide pollution sources.
Experimental Study on Thermal Runaway of LiFePO4/C Battery under Heating Condition
Authors: Gao Fei , Kai Yang , Wang Congjie , Liu Wei , Zhu Yanli
Published: August 2020

The safety of lithium ion batteries is a hot topic in battery application and research at present. LiFePO4/C batteries are generally believed to be safe and have been widely used. The LiFePO4/C batteries are taken as the research object, the thermal runaway characteristics of the LiFePO4/C batteries are analyzed from the changes of battery temperature and voltage during the test process. The results show that the battery volatge fluctuated greatly before the thermal runaway occurred for the battery under one side heating, however, the battery voltage did not fluctuate and dropt to 0 V for the battery under two sides heating. For the battery group under one side heating, the thermal runaway chain reaction did not occur, which meant that the LiFePO4/C battery possessed good safety.
Degradation of Orange I by the zero-valent iron/hydrogen peroxide system
Authors: Zhou Jian , Hou Meifang
Published: August 2020

The zero-valent iron/hydrogen peroxide system was very effective for the oxidative degradation of high concentration Orange I solution. The effects of Orange I initial concentration, hydrogen peroxide concentration, zero-valent iron dosage and pH value of solution on the degradation of Orange I were studied in this article. The concentration of iron ion, pH value and the content of Orange I in the reaction solution were determined by UV-VIS spectrophotometer and pH meter, respectively. The intermediate degradation products were determined by LC-MS. The experimental results showed that the Orange I solution with high concentration could be effectively degraded with low hydrogen peroxide concentration and iron powder dosage under acid condition. In addition, it can be speculated that in the process of degradation, Orange I was first dissociated into 4-(4-hydroxy-1-naphthylazo) benzenesulfonate, and then its chromophore was oxidized and broken, decoloring the reaction solution, followed by the generation to benzene sulfonate, nitrogen and 1, 4-naphthoquinone. After that, 1, 4-naphthoquinone was further oxidized to phthalate.
Experimental Study on the Mechanical Properties of C40 Self-Compacting Solid Ferrous Tailings Concrete
Authors: Zhou Shuangshuang , Liu Jinghong
Published: August 2020

Through the experiments on the mechanical properties of the self-compacting solid ferrous tailings concrete, it studied the effect of tailings powders under various substitution rates upon the mechanical properties of C40 self-compacting solid ferrous tailings concrete. By experiments on the slump expansibility and expansion time T500 of the self-compacting solid tailings concrete, it also studied the effect on the workability of the ferrous tailings powder under various substitution rates. In the light of the experimental results, it provided that, the slump expansibility of the self-compacting solid ferrous tailings concrete enlarged by degrees with the increase of substitution rate of the ferrous tailings powder; the expansion time T500 shortened as the substitution rate of the ferrous tailings powder increased. The cubic compressive strength, the axis compressive strength, the splitting tensile strength as well as the plastic modulus of the self-compacting solid ferrous tailings concrete all inclined to decrease with the swell of substitution rate of the ferrous tailings powder.
Dynamic disturbance damage of rock mass in layered blasting of deep underground plant
Authors: Liang Wu , Tianci Li , Xiaorui Xiang , Jiayi HU
Published: August 2020

This paper established a constitutive model for rock dynamic tension based on HJC and TCK, and achieved the material model embedding through the LS-DYNA UMAT secondary development module analyzed the effect of blasting load, in-situ stress unloading and coupled load on damage distribution of surrounding rock of factory building during layered excavation. Studies have shown that the damage degree of the surrounding rock near the outline of the plant is the largest during the blasting excavation of deep underground powerhouses; when the in-situ stress level is low, the surrounding rock damage near the excavation surface is mainly affected by the blasting load, when the in-situ stress level is high, the surrounding rock damage near the excavation surface caused by the blasting load will be squeezed by the ground stress; in the remote excavated area, the surrounding rock damage is mainly caused by the redistribution of in-situ stress.
The improved analytic hierarchy process (ahp) based on accident tree is applied to the study of community gas risk assessment
Authors: Wen Zhang Zheng
Published: August 2020

Gas safety is related to every family in the community. In this paper, the structural importance in the accident tree is taken as the basis of analytic hierarchy process (ahp) judgment matrix. The improved ahp reduces human subjectivity. It is hoped to provide some reference for the risk assessment of gas leakage accident.
Simulation Verification of Phased Array Ultrasonic Detection Scheme for Wind Turbine Main Shaft in Service
Authors: Xu Zhengbin
Published: August 2020

The main shaft is the key link in the wind turbine drive. Based on the previous scheme design of phased array ultrasonic testing of wind turbine and the results of transducer parameter range determined, simulation verification is carried out in this study. It is verified that the preliminary theoretical design scheme can effectively detect the early defects of the main shaft shoulder position of the wind turbine, which lays a good foundation for the field implementation in the future.
Analysis of micro-friction stir welding surfaces using fractal methodologies
Authors: Prajapati Deepak K , Ahmed Shuja
Published: August 2020

The weld surface produced by micro-friction stir welding (micro-FSW) exhibit multi-scale nature. The surface topography of weld surfaces affects the overall strength of components and significantly changes with process parameters. In this work, multi-scale surface characterization techniques are used to study the surface topography of micro-FSW surfaces. The relation between process parameters and topography parameters is discussed in detail. Length-scale fractal analysis is employed on micro-FSW surfaces, and it is concluded that surface complexity increases with an increase in tool rotational speed. Within the range of process parameters studied, smoothening takes place at higher tool feed. The Hurst coefficient (H), which is an important descriptor of fractal geometry is found to increase with an increase in tool feed.
Fractional quantum Hall effect in CVD-grown graphene
Authors: Schmitz M , Ouaj T , Winter Z , Rubi K , Watanabe K , Taniguchi T , Zeitler U , Beschoten B , Stampfer C
Published: August 2020

We show the emergence of fractional quantum Hall states in graphene grown by chemical vapor deposition (CVD) for magnetic fields from below 3 T to 35 T where the CVD-graphene was dry-transferred. Effective composite-fermion filling factors up to ν
* = 4 are visible and higher order composite-fermion states (with four flux quanta attached) start to emerge at the highest fields. Our results show that the quantum mobility of CVD-grown graphene is comparable to that of exfoliated graphene and, more specifically, that the p/3 fractional quantum Hall states have energy gaps of up to 30 K, well comparable to those observed in other silicon-gated devices based on exfoliated graphene.
Reducing autocorrelation times in lattice simulations with generative adversarial networks
Authors: Pawlowski Jan M , Urban Julian M
Published: August 2020

Short autocorrelation times are essential for a reliable error assessment in Monte Carlo simulations of lattice systems. In many interesting scenarios, the decay of autocorrelations in the Markov chain is prohibitively slow. Generative samplers can provide statistically independent field configurations, thereby potentially ameliorating these issues. In this work, the applicability of neural samplers to this problem is investigated. Specifically, we work with a generative adversarial network (GAN). We propose to address difficulties regarding its statistical exactness through the implementation of an overrelaxation step, by searching the latent space of the trained generator network. This procedure can be incorporated into a standard Monte Carlo algorithm, which then permits a sensible assessment of ergodicity and balance based on consistency checks. Numerical results for real, scalar φ
4-theory in two dimensions are presented. We achieve a significant reduction of autocorrelations while accurately reproducing the correct statistics. We discuss possible improvements to the approach as well as potential solutions to persisting issues.
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function
Authors: Villegas-Morcillo Amelia , Makrodimitris Stavros , van Ham Roeland C H J , Gomez Angel M , Sanchez Victoria , Reinders Marcel J T
Published: August 2020

Motivation

Protein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence representations and predict function from these. Deep supervised models require a lot of labeled training data which are not available for this task. However, a very large amount of protein sequences without functional labels is available.

Results

We applied an existing deep sequence model that had been pretrained in an unsupervised setting on the supervised task of protein molecular function prediction. We found that this complex feature representation is effective for this task, outperforming hand-crafted features such as one-hot encoding of amino acids, k-mer counts, secondary structure and backbone angles. Also, it partly negates the need for complex prediction models, as a two-layer perceptron was enough to achieve competitive performance in the third Critical Assessment of Functional Annotation benchmark. We also show that combining this sequence representation with protein 3D structure information does not lead to performance improvement, hinting that 3D structure is also potentially learned during the unsupervised pretraining.

Availability and implementation

Implementations of all used models can be found at https://github.com/stamakro/GCN-for-Structure-and-Function.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mechanistic insights into SARS-CoV-2 epidemic via revealing the features of SARS-CoV-2 coding proteins and host responses upon its infection
Authors: Qin Shijie , Xia Xinyi , Shi Xuejia , Ji Xinglai , Ma Fei , Chen Liming
Published: August 2020

There are seven known coronaviruses that infect humans: four mild coronaviruses, including HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1, only cause mild respiratory diseases, and three severe coronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2, can cause severe respiratory diseases even death of infected patients. Both infection and death caused by SARS-CoV-2 are still rapidly increasing worldwide. In this study, we demonstrate that viral coding proteins of SARS-CoV-2 have distinct features and are most, medium and least conserved with SARS-CoV, MERS-CoV and the rest four mild coronaviruses (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1), respectively. Moreover, expression of host responsive genes (HRG), HRG-enriched biological processes and HRG-enriched KEGG pathways upon infection of SARS-CoV-2 shows slightly overlapping with SARS-CoV and MERS-CoV but distinctive to the four mild coronaviruses. Interestingly, enrichment of overactivation of neutrophil by HRGs is only and commonly found in infections of severe SARS-CoV-2, SARS-CoV and MERS-CoV but not in the other four mild coronaviruses, and the related gene networks show different patterns. Clinical data support that overactivation of neutrophil for severe patients can be one major factor for the similar clinical symptoms observed in SARS-CoV-2 infection compared to infections of the other two severe coronavirus (SARS-CoV and MERS-CoV). Taken together, our study provides a mechanistic insight into SARS-CoV-2 epidemic via revealing the conserved and distinct features of SARS-CoV-2, raising the critical role of dysregulation of neutrophil for SARS-CoV-2 infection.

Availability and Implementation

All data sources and analysis methods related to this manuscript are available in the methods, supplementary materials and GEO database (https://www.ncbi.nlm.nih.gov/geo/).

Supplementary information

Supplementary data are available at Bioinformatics online.
ipDMR: identification of differentially methylated regions with interval P-values
Authors: Xu Zongli , Xie Changchun , Taylor Jack A , Niu Liang
Published: August 2020

ipDMR is an R software tool for identification of differentially methylated regions (DMRs) using auto-correlated P-values for individual CpGs from epigenome-wide association analysis using array or bisulfite sequencing data. It summarizes P-values for adjacent CpGs, identifies association peaks and then extends peaks to find boundaries of DMRs. ipDMR uses BED format files as input and is easy to use. Simulations guided by real data found that ipDMR outperformed current available methods and provided slightly higher true positive rates and much lower false discovery rates.

Availability and implementation

ipDMR is available at https://bioconductor.org/packages/release/bioc/html/ENmix.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Integrating genomic correlation structure improves copy number variations detection
Authors: Luo Xizhi , Qin Fei , Cai Guoshuai , Xiao Feifei
Published: August 2020

Motivation

Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e. boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions, such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs, which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic dependence structure (i.e. LD).

Results

We theoretically demonstrated the correlation structure of CNV data in SNP array, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. Therefore, we developed the LDcnv that integrated the genomic correlation structure with a local search strategy into statistical modeling of the CNV intensities. To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presented high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. This new segmentation algorithm has a wide scope of potential application with data from various high-throughput technology platforms.

Availability and implementation

https://github.com/FeifeiXiaoUSC/LDcnv.

Supplementary information

Supplementary data are available at Bioinformatics online.
Racial Microaggressions at Work: Reflections from Black African Professionals in Australia
Authors: Gatwiri Kathomi
Published: August 2020

Theorising how race and Africanness intersect in the professional lives of African immigrants can provide a nuanced understanding of how racial identities shape the professional identities of Black Africans in Australia. This article is contextualised within a larger study that sought to explore the Afro-diasporic experiences of highly skilled Black African immigrants in South Australia. Particularly, it examines how Black African professionals experience their workplace. Data were collected through face-to-face semi-structured interviews with twenty-seven Black African professionals in South Australia. The findings from this study reveal that the often-accepted narrative of race-free workplaces is not one that is supported by Black African immigrants’ experiences, as they report constant, subtle and covert patterns of racial microaggressions in the workplace. Utilising critical race theories, this article makes the invisibility of microaggressions visible by probing how the Black body is worn as a burden in the workplace, which consequently produces psychological distress and racial battle fatigue. This study will provide social work practitioners with a critical understanding of the various challenges facing African professionals in the workplace, and how processes of racialisation at work may impact on psychological safety in this environment.
Long-Term Music Exposure Prevents Age-Related Cognitive Deficits in Rats Independently of Hippocampal Neurogenesis
Authors: Rizzolo Lou , Leger Marianne , Corvaisier Sophie , Groussard Mathilde , Platel Hervé , Bouet Valentine , Schumann-Bard Pascale , Freret Thomas
Published: August 2020

Cognitive decline appears across aging. While some studies report beneficial effects of musical listening and practice on cognitive aging, the underlying neurobiological mechanisms remain unknown. This study aims to determine whether chronic (6 h/day, 3 times/week) and long-lasting (4–8 months) music exposure, initiated at middle age in rats (15 months old), can influence behavioral parameters sensitive to age effects and reduce age-related spatial memory decline in rats. Spontaneous locomotor, circadian rhythmic activity, and anxiety-like behavior as well as spatial working and reference memory were assessed in 14-month-old rats and then after 4 and 8 months of music exposure (19 and 23 months old, respectively). Spatial learning and reference memory data were followed up by considering cognitive status of animals prior to music exposure (14 months old) given by K-means clustering of individual Z-score. Hippocampal cell proliferation and brain-derived neurotrophic factor (BDNF) level in the hippocampus and frontal cortex were measured. Results show that music exposure differentially rescues age-related deficits in spatial navigation tasks according to its duration without affecting spontaneous locomotor, circadian rhythmic activity, and anxiety-like behavior. Hippocampal cell proliferation as well as hippocampal and frontal cortex BDNF levels was not affected by music across aging. Cognitive improvement by music in aging rats may require distinct neurobiological mechanisms than hippocampal cell proliferation and BDNF.
Is There a Correlation Between the Number of Brain Cells and IQ?
Authors: Songthawornpong Nicharatch , Teasdale Thomas W , Olesen Mikkel V , Pakkenberg Bente
Published: August 2020

Our access to a unique material of postmortem brains obtained from decades of data collection enabled a stereological analysis of the neuron numbers and correlation of results with individual premorbid intelligence quotient (IQ) data. In our sample of 50 brains from men, we find that IQ does not correlate with the number of brain cells in the human neocortex and was only weakly correlated to brain weight. Our stereological examination extended to measures of several other parameters that might be of relevance to intelligence, including numbers of cerebral glial cells (astrocytes, oligodendrocytes, and microglia) and the volume of key areas in the gray and white matter and of the cerebral ventricles, also showing near-zero nonsignificant correlations to IQ.
Coronavirus Disease 2019 (COVID-19) Infections Among Healthcare Workers, Los Angeles County, February–May 2020
Authors: Hartmann Stacy , Rubin Zachary , Sato Heidi , O Yong Kelsey , Terashita Dawn , Balter Sharon
Published: August 2020

Across the world, healthcare workers (HCW) are at a greater risk of infection by coronavirus disease 2019 (COVID-19) due to the nature of their work. The Los Angeles County Department of Public Health (LAC DPH) set out to understand the impact of COVID-19 on healthcare facilities and HCWs by tracking and analyzing data from case-patient interviews of HCWs. As of 31 May, over 3 months into the pandemic, nearly 5500 positive HCWs were reported to LAC DPH, representing 9.6% of all cases. Cases reported working in 27 different setting types, including outpatient medical offices, correctional facilities, emergency medical services, and so forth, with the highest proportion from long-term care facilities (46.6%) and hospitals (27.7%). Case patients included both clinical and nonclinical roles, with nearly half (49.4%) of positive HCWs being nurses. Over two-thirds of HCWs (68.6%) worked at some point during their infectious period, and nearly half (47.9%) reported a known exposure to a positive patient and/or coworker within their facility. Overall, compared to all LAC cases, HCWs reported lower rates of hospitalization (5.3% vs 12.2%) and death (0.7% vs 4.3%) from COVID-19. There are many factors that increase HCWs risk of infection, including high-risk work environment, limited supply of personal protective equipment, and even pressure to help and work during a pandemic. In response to these data, LAC DPH created resources and provided guidance for healthcare facilities to best protect their patients and staff during the COVID-19 pandemic.
Querying Tenuous Group in Attributed Networks
Authors: Li Yang , Sun Heli , He Liang , Huang Jianbin , Chen Jiyin , He Hui , Jia Xiaolin
Published: August 2020

Finding groups in networks is very common in many practical applications, and most work mainly focus on dense groups. However, in scenarios like reviewer selection or weak social friends recommendation, we need to emphasize the privacy of individuals or minimize the possibility of information dissemination. So the internal relationship between individuals should be as tenuous as possible, but existing works cannot suit well to the requirement. Some works have focused on finding tenuous groups. However, these works only aim to find the most tenuous group and do not consider containing certain vertices. In this paper, we study the problem of finding tenuous groups in attributed networks that contain specific vertices. We first propose a new problem called Tenuous Attributed Group Query, and a new indicator, k-tenuity, to measure the structural tenuity of a group. Then we propose a method TAG-Basic to find proper groups by gradually selecting the vertices with optimal influence. We further design an advanced method TAG-ADV to improve the efficiency by forming a candidate set before selecting the optimal vertex. Experiment results show that k-tenuity is more effective than other state-of-the-art measurements, and our methods obtain the best result on group quality compared with other benchmark methods.
Developmental Stages of Information and Communication Technology
Authors: Löwstedt Anthony
Published: August 2020

With a media anthropological-philosophical approach to ICT, four convergent developmental stages are distinguished and defined: pictography, ethography, phonography, and prography. They are invented/acquired in this sequence by human individuals as well as the human genus in general. Pictograms were first invented in forager cultures, ethograms in permanently settled village communities, phonograms in the early cities and civilizations of southwest Asia and northeast Africa, and electronic programs in a globalized society under North Atlantic domination. Print is considered as a corollary to phonography. Anthropological contextualization of technologies and institutions and the socio-politico-economic inclusivity and exclusivity of media are highlighted. Since the ‘agricultural revolution’, exclusive as well as inclusive media have accompanied humanity. Lately, inclusive potential has grown again through the accessibility, ubiquity, and convergent depth of prography. However, new challenges to inclusivity, including new forms of surveillance, weaponization of the media and widening wealth disparities, have materialized in the same context.
Impaired cytoplasmic domain interactions cause co-assembly defect and loss of function in the p.Glu293Lys KNCJ2 variant isolated from an Andersen–Tawil syndrome patient
Authors: Déri Szilvia , Borbás János , Hartai Teodóra , Hategan Lidia , Csányi Beáta , Visnyovszki Ádám , Madácsy Tamara , Maléth József , Hegedűs Zoltán , Nagy István , Arora Rohit , Labro Alain J , Környei László , Varró András , Sepp Róbert , Ördög Balázs
Published: August 2020

Aims

Subunit interactions at the cytoplasmic domain interface (CD-I) have recently been shown to control gating in inward rectifier potassium channels. Here we report the novel KCNJ2 variant p.Glu293Lys that has been found in a patient with Andersen–Tawil syndrome type 1 (ATS1), causing amino acid substitution at the CD-I of the inward rectifier potassium channel subunit Kir2.1. Neither has the role of Glu293 in gating control been investigated nor has a pathogenic variant been described at this position. This study aimed to assess the involvement of Glu293 in CD-I subunit interactions and to establish the pathogenic role of the p.Glu293Lys variant in ATS1.

Methods and results

The p.Glu293Lys variant produced no current in homomeric form and showed dominant-negative effect over wild-type (WT) subunits. Immunocytochemical labelling showed the p.Glu293Lys subunits to distribute in the subsarcolemmal space. Salt bridge prediction indicated the presence of an intersubunit salt bridge network at the CD-I of Kir2.1, with the involvement of Glu293. Subunit interactions were studied by the NanoLuc® Binary Technology (NanoBiT) split reporter assay. Reporter constructs carrying NanoBiT tags on the intracellular termini produced no bioluminescent signal above background with the p.Glu293Lys variant in homomeric configuration and significantly reduced signals in cells co-expressing WT and p.Glu293Lys subunits simultaneously. Extracellularly presented reporter tags, however, generated comparable bioluminescent signals with heteromeric WT and p.Glu293Lys subunits and with homomeric WT channels.

Conclusions

Loss of function and dominant-negative effect confirm the causative role of p.Glu293Lys in ATS1. Co-assembly of Kir2.1 subunits is impaired in homomeric channels consisting of p.Glu293Lys subunits and is partially rescued in heteromeric complexes of WT and p.Glu293Lys Kir2.1 variants. These data point to an important role of Glu293 in mediating subunit assembly, as well as in gating of Kir2.1 channels.
Re-Evaluating the Evidence for Faecal Microbiota Transplantation ‘Super-Donors’ in Inflammatory Bowel Disease
Authors: Olesen Scott W , Gerardin Ylaine
Published: August 2020

Background

Faecal microbiota transplantation [FMT] is a recommended treatment for recurrent Clostridioides difficile infection, and there is promise that FMT may be effective for conditions such as inflammatory bowel disease [IBD]. Previous FMT clinical trials have considered the possibility of a ‘donor effect’, that is, that FMT material from different donors has different clinical efficacies.

Methods

Here we re-evaluate evidence for donor effects in published FMT clinical trials for IBD.

Results

In ten of 12 published studies, no statistically significant donor effect was detected when rigorously re-evaluating the original analyses. One study showed statistically significant separation of microbiota composition of pools of donor stool when stratified by patient outcome. One study reported a significant effect but did not have underlying data available for re-evaluation. When quantifying the uncertainty on the magnitude of the donor effect, confidence intervals were large, including both zero donor effects and very substantial donor effects.

Conclusion

Although we found very little evidence for donor effects, the existing data cannot rule out the possibility that donor effects are clinically important. Large clinical trials prospectively designed to detect donor effects are probably needed to determine if donor effects are clinically relevant for IBD.
Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation
Authors: Wallentin Lars , Lindbäck Johan , Eriksson Niclas , Hijazi Ziad , Eikelboom John W , Ezekowitz Michael D , Granger Christopher B , Lopes Renato D , Yusuf Salim , Oldgren Jonas , Siegbahn Agneta
Published: August 2020

Aims

The global COVID-19 pandemic is caused by the SARS-CoV-2 virus entering human cells using angiotensin-converting enzyme 2 (ACE2) as a cell surface receptor. ACE2 is shed to the circulation, and a higher plasma level of soluble ACE2 (sACE2) might reflect a higher cellular expression of ACE2. The present study explored the associations between sACE2 and clinical factors, cardiovascular biomarkers, and genetic variability.

Methods and results

Plasma and DNA samples were obtained from two international cohorts of elderly patients with atrial fibrillation (n = 3999 and n = 1088). The sACE2 protein level was measured by the Olink Proteomics® Multiplex CVD II96 × 96 panel. Levels of the biomarkers high-sensitive cardiac troponin T (hs-cTnT), N-terminal probrain natriuretic peptide (NT-proBNP), growth differentiation factor 15 (GDF-15), C-reactive protein, interleukin-6, D-dimer, and cystatin-C were determined by immunoassays. Genome-wide association studies were performed by Illumina chips. Higher levels of sACE2 were statistically significantly associated with male sex, cardiovascular disease, diabetes, and older age. The sACE2 level was most strongly associated with the levels of GDF-15, NT-proBNP, and hs-cTnT. When adjusting for these biomarkers, only male sex remained associated with sACE2. We found no statistically significant genetic regulation of the sACE2 level.

Conclusions

Male sex and clinical or biomarker indicators of biological ageing, cardiovascular disease, and diabetes are associated with higher sACE2 levels. The levels of GDF-15 and NT-proBNP, which are associated both with the sACE2 level and a higher risk for mortality and cardiovascular disease, might contribute to better identification of risk for severe COVID-19 infection.
Covariation patterns of phytoplankton and bacterioplankton in hypertrophic shallow lakes
Authors: Schiaffino M R , Huber P , Sagua M , Sabio y García C A , Reissig M
Published: August 2020

The aim of this work was to assess the temporal patterns in the community composition of phytoplankton (PCC) and bacterioplankton (BCC) in two interconnected and hypertrophic Pampean shallow lakes in Argentina. Factors shaping their community dynamics and community temporal covariations were also analysed. We performed 4 years of seasonal samplings (2012–2016) and communities were studied by the Utermöhl approach (PCC) and Illumina MiSeq sequencing (BCC). We found marked seasonal variations in both communities and inter-annual variations with decreasing microbial community similarities during the study. We also observed covariation in community-level dynamics among PCC and BCC within and between shallow lakes. The within-lake covariations remained positive and significant, while controlling for the effects of intrinsic (environmental) and extrinsic (temporal and meteorological) factors, suggesting a community coupling mediated by intrinsic biotic interactions. Algal-bacterial associations between different taxa of phytoplankton and bacterioplankton within each lake were also found. PCC was mainly explained by pure regional extrinsic (17–21%) and intrinsic environmental (8–9%) factors, while BCC was explained by environmental (8–10%) and biotic interactions with phytoplankton (7–8%). Our results reveal that the influence of extrinsic regional factors can be channeled to bacterioplankton through both environmental (i.e. water temperature) and phytoplankton effects.
SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping
Authors: Feng Yi , Beh Leslie Y , Chang Wei-Jen , Landweber Laura F
Published: August 2020

Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.