bluuebunny/crossref_metadata_2025 huggingface dataset:
Socio-ecological consequences during the construction of a multistage system of flood control facilities on side tributaries
Authors: Podgornov N S , Davydov R V , Zotov D K , Antonov V I , Maslikov V I , Maslikova E I , Chusov A N , Cheremisin A V
Published: June 2021

A method of protecting territories in a river basin during flash floods by creating a multi-stage system of intercepting flood control systems with temporarily filled reservoirs, with a phased construction of waterworks on side tributaries, including secondary ones. Using the computer programs developed by the authors, the operating modes of the hydroelectric system were simulated for a possible variant of placing their sections on the lateral tributary of the river: in the lower reaches- a traditional hydro system with an earth dam and a concrete spillway, including bottom holes and a surface spillway; upstream- an additional hydro system with a filtering dam made of gabion masonry, into which the missing accumulating volume is redistributed. The calculation of the social effect resulting from the considered method of protection by assessing the reduction of economic damage for settlements located in the downstream of the main flood control hydroelectric complex with participation in the cutoff of the flood peak of an additional temporarily filled reservoir located upstream of the river is performed.
Early diagnostics of productivity and longevity of alfalfa selective samples
Authors: Bekuzarova S A , Lushchenko G V , Gasiev V I
Published: June 2021

The paper provides signs of productivity and longevity at the stage of seedlings, which accelerates selection in the breeding process for important indicators. Correlations between the shape of the root system and longevity, leaf area and productivity have been determined Key words: root system, morphology, productivity, varietal differences.
Study of the physicochemical properties of the biomedical composite material “Ti-Nb-Ta-Zr with a surface polymer layer”
Authors: Nasakina E O , Sevostyanova T M , Alexandrova A G , Kaplan M A , Kolmakova A A , Sudarchikova M A , Sergiyenko K V , Kuznetsova O G , Novikova D A , Shatova L A , Baikin A S
Published: June 2021

A comprehensive study of the physicochemical properties of the created biomedical composite material “Ti-Nb-Ta-Zr with a surface polymer layer” was carried out. The polymer film does not in any way affect the radiopacity of the base material. All materials obtained are radiopaque. X-ray diffraction analysis of polyglycolide lactide (PGLA) samples with molecular weights of 45, 90, 180 kDa showed that the polymers have a completely amorphous structure. On samples with a 40-μm-thick PLA-based coating bare-metal zones are observed, which substantiate anode effects in the potential range of more than 1000 mV.
Influence of ion treatment in the production of thin multilevel surface layers
Authors: Nasakina E O , Sudarchikova M A , Novikova D A , Kurganova Yu A , Fakhurtdinov R S , Baikin A S , Baranov E E , Prutskov M E , Kolmakov A G , Sevostyanov M A
Published: June 2021

The regularities of the formation of titanium and tantalum multilayers with the use of magnetron sputtering and ion bombardment were investigated depending on the varied technological parameters. Metallic composite materials had a multilayer structure. The surface morphology at low radiation doses in the course of preliminary ion etching corresponds to the substrate surface morphology. With a long duration/energy of ion bombardment, a thin surface structure in the form of point depressions is observed, smoothed by a layer deposited from above, and the length of the layer and its crystallinity also increase. The transition layer ensures high adhesion of the surface layer to the substrate.
An air cavity above a complex vortex: an experimental and analytical study of the features of its lower part
Authors: Kistovich A V , Chaplina T O , Stepanova E V
Published: June 2021

The description of the experiments with the water vortex generated in a variety of facilities by means of different activators is presented. The changes in the form and size of the air cavity above such a vortex are studied for different regimes of rotations. An analytical description for the free surface form of the water vortex is given, which is in good agreement with both experimental data and previously obtained relations based on fundamental hydrodynamics equations. The problem of the “spout’s” volume of the air cavity is also considered. It is shown that “spout’s“ volume can be used for calculating of the radius of the water “solid-state” rotation. Estimated calculations of the “spout’s“ volume based on experimental data are made.
Screening of different Fe (II) and Fe (III) complexes at the stage of rhizogenesis in vitro of gooseberry plants
Authors: Nikulina E A , Akimova S V , Tsirulnikova N V , Glinushkin A P , Dolgoborodov I O , Kirkach V V
Published: June 2021

During clonal micropropagation of the Pink-2 (Rosovy-2) gooseberry cultivar at the stage of rhizogenesis, the efficiency of modification of the media with mineral salts according to Quoirin-Lepoivre (QL) was shown by replacing iron, which is standardly used in the form of FeSO4×7H2O together with Na2EDTA, with chelated forms with carboxyl-containing ligands Fe(III)-EDTA and Fe(III)-DTPA and the organophosphate complexone Fe(II)-HEDP. On the 45th and 60th days of subculturing, the distribution in descending order of the impact of chelate iron compounds on the rooting rate of the studied gooseberry plants was as follows: Fe(III)-EDTA>Fe(III)-DTPA> Fe(II)-HEDP> Fe(III)-EDDHA>Fe(III)-HEDP. On the 60th day of subculturing in the best variants of the experiment, the rooting rate of gooseberry microcuttings of cultivar Pink-2 was 86.7-100% compared to 60% in the control variant.
ASSESSMENT OF THE STATE AND RESTORATION OF BIOLOGICAL RESOURCES OF SCOTS PINE (PINUS SILVESTRIS L.) IN THE SOUTH OF THE CENTRAL RUSSIAN UPLAND
Authors: Cherniavskih V I , Dumacheva E V , Markova E I
Published: June 2021

The paper deals with an assessment of the current state and prospects for the creation of artificial forest plantations based on Pinus silvestris L. to increase the bio resource potential of the south of the Central Russian Upland. There have been tested and methodically substantiated various methods of creating long-term forest plantations based on Pinus silvestris L. by improving the methods of sowing seeds. Evaluation of the effectiveness of various methods of sowing pine has shown that more guaranteed and uniform seedlings and further development of seedlings provide sowing with cones. Having an equal number of seed holes when sowing with seeds and cones, it can be stated that the number of holes in which seedlings appeared during sowing with cones is 56.8% higher, the survival rate of seedlings is 34.6% higher, the number of seedlings is 25% higher, and the number plants per hole – by 50%. Sowing with cones is economically more profitable-no need to engage in costly threshing of seeds; cones are easier to plant during mass plantings in the process of laying artificial forest plantations; cones have a high hygroscopicity, the seeds are constantly in a moist state and germinate well, regardless of the conditions of soil and air moisture.
Composite Soils- the Basis for Sustainable Agricultural Development
Authors: Glihushkin A P , Sviridova L L , Sycheva I I , Grishina E V , Sevostyanov M A
Published: June 2021

The article reviews scientific publications on artificial soils. The ambiguity of this thematic problem is a great interest to the world community as resource endowment on a planetary scale is declining without the right to recovery. Humanity as a whole has no choice but to think of scientifically based concepts to recreate the conditions for survival. The paper describes the main directions of combining soil mixtures, developed technologies of application, results of influence of composite materials on plant growth functions.
Development of an optical system for lighting rooms with biologically safe and environmentally friendly sunlight
Authors: Gureeva I M , Briushinin A A , Savin D D , Diuldin M V
Published: June 2021

The article discusses the development and advantages of an optical system for lighting rooms with biologically safe and environmentally friendly sunlight. A passive system that does not consume energy is proposed. The analysis of artificial light sources by their spectral composition is carried out. It was found that the spectral composition most suitable for a comfortable human condition is an incandescent lamp, which has several limitations. It is established that the most environmentally friendly and safe solution is the use of sunlight. An energy-efficient natural light system has been developed, creating a comfortable environment for the eyes, well-being, and mood of a person.
Monitoring the state of flowing water in purification and water supply systems
Authors: Isakov F A , Svyatkina V I , Diuldin M V
Published: June 2021

The article substantiates the need to control water at various stages of its purification before consumption. Several stages of water purification in the city of St. Petersburg are considered. The advantages and disadvantages of the used water control system are noted. Various options for monitoring the state of water in the pipeline between cleaning cycles are considered. The advantages of using a refractometer for monitoring the purity (quality) of water are shown.
The method of increasing the accuracy of coordinates of the contaminated area and water surfaces during environmental monitoring
Authors: Kulikova M E , Nagornaya A I , Diuldin M V
Published: June 2021

One of the methods for increasing the accuracy of compiling pollution maps based on the results of air and ground monitoring of environmental monitoring of territories is considered. It has been substantiated that for the study of large areas it is advisable to install equipment for monitoring the state of the environment on aircraft. To improve the accuracy of determining coordinates in difficult conditions, it is proposed to use a quasi-differential mode of operation of navigation equipment placed on an aircraft in the developed method. The aircraft is equipped with various equipment and moves at high speed, conducting research on large areas of the territory. At an aircraft speed of more than 250 km / h, the accuracy of determining the coordinates of 30 m for drawing up an ecological map on a large scale suits the services responsible for environmental safety. Based on these data, additional environmental monitoring is carried out only in areas where pollution is detected. This reduces the time for complete environmental monitoring and saves material resources.
The impact of the ecological state of the region of birth on the functional state of health
Authors: Mazing M S , Zaitceva A Y , Diuldin M V
Published: June 2021

The paper considers the problem of the impact of a complex of environmental factors and their impact on the health of young people. Young people aged 18 to 21 years old, who lived up to 18 years old in different environmental conditions, were examined in order to assess the general functional state of their body. The study used a developed non-invasive optical method for assessing the oxygen status of tissues and general functional state, as well as an independent biomedical study. The results of the experiment revealed the significance of the influence of the ecological factors of the region of birth on the functional state of health of the young generation.
Efficient treatment of wastewater from galvanic plants
Authors: Cheremisin A V , Valiullin L R , Myazin N S , Logunov S E
Published: June 2021

The article discusses a promising method for the purification of chromium-containing wastewater from galvanic plants. A review and comparative analysis of existing methods and technologies for treatment of industrial waste from various organochromium compounds, such as reagent-based, biological, ion-exchange and others, are presented. The advantages of using the combined method of chromium-containing wastewater treatment based on electroflotation with preliminary electrocoagulation are shown. The effectiveness of the proposed combined method is evaluated and the design of electroflotocoagulator is developed.
Environmental monitoring of workplace lighting using optical Internet
Authors: Savin D D , Gureeva I M , Briushinin A A , Diuldin M V
Published: June 2021

The article shows the need for efficient use of electric energy in order to preserve the resources and environmental health of the planet. The necessity of the modernization of existing systems control the ambient light in the area of jobs solution to the problems of ecology eyes. The method of control and adjustment of illumination of workplaces and zones where it, is necessary is offered. A control system using the optical Internet has been developed. The simulation of the system operation was carried out, the possible amounts of saving electric energy, natural resources and reducing the negative impact on the environment were determined.
An integrated approach to the study of ecosystem state for soil and vegetation cover of urban areas
Authors: Cheremisin A V , Chusov A N , Fedorov M P , Switala F , Valiullin L R , Shurupov D N
Published: June 2021

The article substantiates the need for a comprehensive assessment of the state of the ecosystem. To do this, it is necessary to perform studies of the state of the soil, water and vegetation cover using various devices. The studies were carried out both in a stationary laboratory using samples taken from the territory, and in the field using devices for express control. For additional control of the vegetation cover, the results of video filming and research carried out using a thermal imager and radar stations were used. The latter method is extremely effective if the soil or plants contain large amounts of radioactive substances or heavy metals. For research, previously compiled maps of contamination of territories using GIS technologies were used. Comparison of these data will help to establish the causal factors of pollution. In addition, it is possible to identify the migration of pollution under the influence of various climatic phenomena, etc. The use of high-resolution instruments (for example, an X-ray spectrometer or a power optical microscope) allows one to determine the entire spectrum of contamination in soil, water and on plant samples. This allows in the future to assess the behavior of chemical elements in the “soil-plant” system to determine the possibility of cleaning the area using plants. Of particular interest is the burning of fallen leaves with burying waste in the ground.
Assessment of risk, damage and environmental safety of emergency situations at energy facilities
Authors: Lukashev N A , Valov A P , Arinushkina K G , Diuldin M V
Published: June 2021

It has been substantiated that the most stable source of energy at any time are nuclear power plants and hydroelectric power plants. It is noted that these sources of electric power generation are the most dangerous in the event of an emergency for nature and humans. In addition, nuclear power generates dangerous sources of pollution during its operation. The article compares the levels of pollution emanating from traditional energy sources and nuclear power plants.
Investigation of the structure and mechanical properties of stainless steel alloyed with silver
Authors: Kaplan M A , Ivannikov A Yu , Gorbenko A D , Mikhailova A V , Kirsankin A A , Kalaida T A , Konushkin S V , Sevostyanov M A
Published: June 2021

The paper contains information of the development of technology for smelting stainless steel for application in the manufacture of medical devices. Smelting was carried out in electric arc vacuum furnaces. The technology has been developed for producing sheets with a thickness of 1 ÷ 1.25 mm for further research of mechanical properties. To study the structure, thin sections of the alloys were obtained by melting and further rolling. The mechanical properties of the samples and their structure have been studied. The results show that the addition of a small amount of silver decreases the mechanical properties of the steel. In the ingots, a dendritic structure is observed, and after warm rolling, the structure has a pronounced fine-grained austenitic structure.
Electromagnetic effects of equatorially misaligned RF cavities
Authors: Karatay A. , Yaman F.
Published: June 2021

One of the most challenging problems in modern particle accelerator systems is the manufacture of RF cavities within the desired tolerance limits. In this study experimental and computational investigations to quantify the effects of transversal half-cell misalignments on the fundamental accelerator cavity parameters and beam dynamics are presented. Equivalent circuit components of an equatorially misaligned single-cell aluminum elliptical cavity are obtained from the measured data and are employed to calculate longitudinal impedance and modal wake function. Critical coupling and bead-pull measurements are performed at the TM010-like mode frequency, 2.45 GHz for the quality factor and shunt impedance of the high-β cavity. We report equivalent circuit analysis for higher-order modes and variations of the equivalent circuit components with respect to considered misalignment errors for the MICE experiment's muon cooling cavity. It is shown that using the equivalent circuit model decreases the computational load significantly for the wake field simulations of resonator cavities. Good agreement between simulations and measurements in terms of accelerating cavity parameters and impedances is illustrated.
Efficient description of experimental effects in amplitude analyses
Authors: Mathad A. , O'Hanlon D. , Poluektov A. , Rabadan R.
Published: June 2021

Amplitude analysis is a powerful technique to study hadron decays. A significant complication in these analyses is
the treatment of instrumental effects, such as background and selection efficiency variations, in the multidimensional
kinematic phase space. This paper reviews conventional methods to estimate efficiency and background
distributions and outlines the methods of density estimation using Gaussian processes and artificial neural networks.
Such techniques see widespread use elsewhere, but have not gained popularity in use for amplitude analyses.
Finally, novel applications of these models are proposed, to estimate background density in the signal region from the sidebands in multiple dimensions, and a more general method for model-assisted density estimation using artificial neural networks.
A comparative analysis of green financial policy output in OECD countries
Authors: Steffen Bjarne
Published: June 2021

The mitigation of dangerous climate change requires massive investments in low-carbon technologies. Accordingly, the redirection of finance flows is a key objective of the Paris Agreement, and countries have started to enact policies to influence financial actors to this end. However, transparency on such policies is low, and it is hardly possible to compare policy activity internationally. To fill this gap, here we present a comparative analysis of green financial policy output in OECD countries from 2001 to 2019, based on a newly compiled inventory of 136 policies from 29 countries and the European Union. We show that policy output accelerated rapidly since the Paris Agreement, with countries implementing 3.3 policies on average using various governing resources. Key instruments include carbon disclosure requirements, low-carbon investment policies for public funds, and green state investment banks. However, there are huge differences in policy output between countries, and some countries that host important financial centers have implemented few policies to date. On the basis of our results, we develop a research agenda to deepen the understanding of this important but little-studied area of climate policies.
A wrinkled ZnO/MCM-41 nanocomposite: hydrothermal synthesis and characterization
Authors: Panecatl-Bernal Yesmin , Juárez Rodolfo Lima , de Vasconcelos Elder Alpes , Chávez Portillo Melissa , de Azevedo Walter Mendes , Méndez-Rojas Miguel-Ángel , Garrido-Rosado Rafael , Villanueva-Cab Julio , Iniesta Salvador Alcántara , Alvarado Joaquín
Published: June 2021

ZnO/MCM-41 composites consisting of loose particles with an irregular, wrinkled surface and flower-like morphology were obtained by adding MCM-41 to a mixture of zinc nitrate hexahydrate and hexamethylenetetramine under hydrothermal conditions. The physical properties of this composite were determined by scanning electron microscopy (SEM), x-ray powder diffraction (XRD), Fourier Transform Infrared spectroscopy (FTIR), and photoluminescence spectroscopy (PL). The XRD analysis showed the characteristic diffractogram corresponding to silica overlapped with ZnO peaks, with a reduction in the sharpness and peak intensity, which may be the result of spatial disorder and defects, combined with anisotropic preferential growth. The FTIR spectrum had the characteristic vibrations expected for a silica framework, containing adsorbed water molecules, nitrate ions, and Zn–O bonds. This novel structure may be of particular interest from both fundamental and applied perspectives. It can be advantageous for the adsorption and capture of small molecules. Therefore, it may improve the performance of some previously investigated uses for these ZnO/MCM-41composites, such as photocatalysis and adsorbents for pollutants removal. To the best of our knowledge, this is the first time that wrinkled ZnO/MCM-41 nanocomposite obtained by a low-cost and easy method is reported.
Chromatin loop anchors predict transcript and exon usage
Authors: Zhang Yu , Cai Yichao , Roca Xavier , Kwoh Chee Keong , Fullwood Melissa Jane
Published: June 2021

Epigenomics and transcriptomics data from high-throughput sequencing techniques such as RNA-seq and ChIP-seq have been successfully applied in predicting gene transcript expression. However, the locations of chromatin loops in the genome identified by techniques such as Chromatin Interaction Analysis with Paired End Tag sequencing (ChIA-PET) have never been used for prediction tasks. Here, we developed machine learning models to investigate if ChIA-PET could contribute to transcript and exon usage prediction. In doing so, we used a large set of transcription factors as well as ChIA-PET data. We developed different Gradient Boosting Trees models according to the different tasks with the integrated datasets from three cell lines, including GM12878, HeLaS3 and K562. We validated the models via 10-fold cross validation, chromosome-split validation and cross-cell validation. Our results show that both transcript and splicing-derived exon usage can be effectively predicted with at least 0.7512 and 0.7459 of accuracy, respectively, on all cell lines from all kinds of validations. Examining the predictive features, we found that RNA Polymerase II ChIA-PET was one of the most important features in both transcript and exon usage prediction, suggesting that chromatin loop anchors are predictive of both transcript and exon usage.
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx
Authors: Ko Seyoon , Li Ginny X , Choi Hyungwon , Won Joong-Ho
Published: June 2021

Statistical analysis of ultrahigh-dimensional omics scale data has long depended on univariate hypothesis testing. With growing data features and samples, the obvious next step is to establish multivariable association analysis as a routine method to describe genotype–phenotype association. Here we present ParProx, a state-of-the-art implementation to optimize overlapping and non-overlapping group lasso regression models for time-to-event and classification analysis, with selection of variables grouped by biological priors. ParProx enables multivariable model fitting for ultrahigh-dimensional data within an architecture for parallel or distributed computing via latent variable group representation. It thereby aims to produce interpretable regression models consistent with known biological relationships among independent variables, a property often explored post hoc, not during model estimation. Simulation studies clearly demonstrate the scalability of ParProx with graphics processing units in comparison to existing implementations. We illustrate the tool using three different omics data sets featuring moderate to large numbers of variables, where we use genomic regions and biological pathways as variable groups, rendering the selected independent variables directly interpretable with respect to those groups. ParProx is applicable to a wide range of studies using ultrahigh-dimensional omics data, from genome-wide association analysis to multi-omics studies where model estimation is computationally intractable with existing implementation.
The DNA methylation haplotype (mHap) format and mHapTools
Authors: Zhang Zhiqiang , Dan Yuhao , Xu Yaochen , Zhang Jiarui , Zheng Xiaoqi , Shi Jiantao
Published: June 2021

Bisulfite sequencing (BS-seq) is currently the gold standard for measuring genome-wide DNA methylation profiles at single-nucleotide resolution. Most analyses focus on mean CpG methylation and ignore methylation states on the same DNA fragments [DNA methylation haplotypes (mHaps)]. Here, we propose mHap, a simple DNA mHap format for storing DNA BS-seq data. This format reduces the size of a BAM file by 40- to 140-fold while retaining complete read-level CpG methylation information. It is also compatible with the Tabix tool for fast and random access. We implemented a command-line tool, mHapTools, for converting BAM/SAM files from existing platforms to mHap files as well as post-processing DNA methylation data in mHap format. With this tool, we processed all publicly available human reduced representation bisulfite sequencing data and provided these data as a comprehensive mHap database.

Availability and implementation

https://jiantaoshi.github.io/mHap/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Perioperative mortality in bariatric surgery: meta-analysis
Authors: Robertson A G N , Wiggins T , Robertson F P , Huppler L , Doleman B , Harrison E M , Hollyman M , Welbourn R
Published: June 2021

Background

Bariatric surgery is an established treatment for severe obesity; however, fewer than 1 per cent of eligible patients undergo surgery. The perceived risk of surgery may contribute to the low uptake. The aim of this study was to determine perioperative mortality associated with bariatric surgery, comparing different operation types and data sources.

Methods

A literature search of Ovid MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials was conducted to identify studies published between 1 January 2014 and 31 July 2020. Inclusion criteria were studies of at least 1000 patients reporting short-term mortality after bariatric surgery. Data were collected on RCTs. Meta-analysis was performed to establish overall mortality rates across different study types. The primary outcome measure was perioperative mortality. Different operation types were compared, along with study type, in subgroup analyses. The study was registered at PROSPERO (2019: CRD 42019131632).

Results

Some 4356 articles were identified and 58 met the inclusion criteria. Data were available on over 3.6 million patients. There were 4707 deaths. Pooled analysis showed an overall mortality rate of 0.08 (95 per cent c.i. 0.06 to 0.10; 95 per cent prediction interval 0 to 0.21) per cent. In subgroup analysis, there was no statistically significant difference between overall, 30-day, 90-day or in-hospital mortality (P = 0.29). There was no significant difference in reported mortality for RCTs, large studies, national databases or registries (P = 0.60). The pooled mortality rates by procedure type in ascending order were: 0.03 per cent for gastric band, 0.05 per cent for sleeve gastrectomy, 0.09 per cent for one-anastomosis gastric bypass, 0.09 per cent for Roux-en-Y gastric bypass, and 0.41 per cent for duodenal switch (P < 0.001 between operations).

Conclusion

Bariatric surgery is safe, with low reported perioperative mortality rates.
MOG autoantibodies trigger a tightly-controlled FcR and BTK-driven microglia proliferative response
Authors: Pellerin Kathryn , Rubino Stephen J , Burns Jeremy C , Smith Benjamin A , McCarl Christie-Ann , Zhu Jing , Jandreski Luke , Cullen Patrick , Carlile Thomas M , Li Angela , Rebollar Jorge Vera , Sybulski Jennifer , Reynolds Taylor L , Zhang Baohong , Basile Rebecca , Tang Hao , Harp Chelsea Parker , Pellerin Alex , Silbereis John , Franchimont Nathalie , Cahir-McFarland Ellen , Ransohoff Richard M , Cameron Thomas O , Mingueneau Michael
Published: June 2021

Autoantibodies are a hallmark of numerous neurological disorders, including multiple sclerosis, autoimmune encephalitides and neuromyelitis optica. Whilst well understood in peripheral myeloid cells, the pathophysiological significance of autoantibody-induced Fc receptor signalling in microglia remains unknown, in part due to the lack of a robust in vivo model. Moreover, the application of therapeutic antibodies for neurodegenerative disease also highlights the importance of understanding Fc receptor signalling in microglia.

Here, we describe a novel in vivo experimental paradigm that allows for selective engagement of Fc receptors within the CNS by peripherally injecting anti-myelin oligodendrocyte glycoprotein (MOG) monoclonal antibodies into normal wild-type mice.

MOG antigen-bound immunoglobulins were detected throughout the CNS and triggered a rapid and tightly regulated proliferative response in both brain and spinal cord microglia. This microglial response was abrogated when anti-MOG antibodies were deprived of Fc receptor effector function or injected into Fcγ receptor knockout mice and was associated with the downregulation of Fc receptors in microglia, but not peripheral myeloid cells, establishing that this response was dependent on central Fc receptor engagement. Downstream of the Fc receptors, BTK was a required signalling node for this response, as microglia proliferation was amplified in BtkE41K knock-in mice expressing a constitutively active form of the enzyme and blunted in mice treated with a CNS-penetrant small molecule inhibitor of BTK. Finally, this response was associated with transient and stringently regulated changes in gene expression predominantly related to cellular proliferation, which markedly differed from transcriptional programs typically associated with Fc receptor engagement in peripheral myeloid cells.

Together, these results establish a physiologically-meaningful functional response to Fc receptor and BTK signalling in microglia, while providing a novel in vivo tool to further dissect the roles of microglia-specific Fc receptor and BTK-driven responses to both pathogenic and therapeutic antibodies in CNS homeostasis and disease.
Illusory Body Ownership Affects the Cortical Response to Vicarious Somatosensation
Authors: Pamplona Gustavo S P , Salgado Julio A D , Staempfli Philipp , Seifritz Erich , Gassert Roger , Ionta Silvio
Published: June 2021

Fundamental human feelings such as body ownership (“this” body is “my” body) and vicariousness (first-person-like experience of events occurring to others) are based on multisensory integration. Behavioral links between body ownership and vicariousness have been shown, but the neural underpinnings remain largely unexplored. To fill this gap, we investigated the neural effects of altered body ownership on vicarious somatosensation. While recording functional brain imaging data, first, we altered participants’ body ownership by robotically delivering tactile stimulations (“tactile” stroking) in synchrony or not with videos of a virtual hand being brushed (“visual” stroking). Then, we manipulated vicarious somatosensation by showing videos of the virtual hand being touched by a syringe’s plunger (touch) or needle (pain). Only after the alteration of body ownership (synchronous visuo-tactile stroking) and specifically during late epochs of vicarious somatosensation, vicarious pain was associated with lower activation in premotor and anterior cingulate cortices with respect to vicarious touch. At the methodological level, the present study highlights the importance of the neural response’s temporal evolution. At the theoretical level, it shows that the higher-level (cognitive) impact of a lower-level (sensory) body-related processing (visuo-tactile) is not limited to body ownership but also extends to other psychological body-related domains, such as vicarious somatosensation.
Epidemiology of Cervical Adenocarcinoma and Squamous Cell Carcinoma Among Women Living With Human Immunodeficiency Virus Compared With the General Population in the United States
Authors: Rositch Anne F , Levinson Kimberly , Suneja Gita , Monterosso Analise , Schymura Maria J , McNeel Timothy S , Horner Marie-Josephe , Engels Eric , Shiels Meredith S
Published: June 2021

Background

Although cervical cancer risk overall is elevated among women living with human immunodeficiency virus (HIV; WLH), it is unclear whether risks are similarly elevated across histologic subtypes.

Methods

Data from the HIV/AIDS Cancer Match Study, a linkage of 12 US HIV and cancer registries during 1996 -2016, were used. Cervical cancers were categorized as adenocarcinoma (AC), squamous cell carcinoma (SCC), or other histologic subtype. Standardized incidence ratios compared rates of AC and SCC in WLH to those in general population. For WLH, risk factors for AC and SCC were evaluated using Poisson regression. Five-year survival was estimated by HIV status and histology.

Results

Overall, 62 615 cervical cancers were identified, including 609 in WLH. Compared with the general population, incidence of AC was 1.47 times higher (95% confidence interval [CI]: 1.03–2.05) and SCC was 3.62 times higher among WLH (95% CI: 3.31–3.94). Among WLH, there was no difference in AC rates by race/ethnicity or HIV transmission group, although SCC rates were lower among White women (vs Black) and higher among women who inject drugs (vs heterosexual transmission). Among WLH, 5-year overall survival was similar for AC (46.2%) and SCC (43.8%) but notably lower than for women not living with HIV.

Conclusions

Among WLH, AC rates were modestly elevated, whereas SCC rates were greatly elevated compared with the general population. These findings suggest there may be differences in the impact of immunosuppression and HIV in the development of AC versus SCC, given their common etiology in human papillomavirus infection.
Epigenetic Aging Biomarkers Associated With Cognitive Impairment in Older African American Adults With Human Immunodeficiency Virus (HIV)
Authors: Shiau Stephanie , Arpadi Stephen M , Shen Yanhan , Cantos Anyelina , Ramon Christian Vivar , Shah Jayesh , Jang Grace , Manly Jennifer J , Brickman Adam M , Baccarelli Andrea A , Yin Michael T
Published: June 2021

Background

Accelerated epigenetic aging using DNA methylation (DNAm)-based biomarkers has been reported in people with human immunodeficiency virus (HIV, PWH), but limited data are available among African Americans (AA), women, and older PWH.

Methods

DNAm was measured using Illumina EPIC Arrays for 107 (69 PWH and 38 HIV-seronegative controls) AA adults ≥60 years in New York City. Six DNAm-based biomarkers of aging were estimated: (1) epigenetic age acceleration (EAA), (2) extrinsic epigenetic age acceleration (EEAA), (3) intrinsic epigenetic age acceleration (IEAA), (4) GrimAge, (5) PhenoAge, and (6) DNAm-estimated telomere length (DNAm-TL). The National Institutes of Health (NIH) Toolbox Cognition Battery (domains: executive function, attention, working memory, processing speed, and language) and Montreal Cognitive Assessment (MoCA) were administered. Participants were assessed for frailty by the Fried criteria.

Results

The PWH and control groups did not differ by sex, chronological age, or ethnicity. In total, 83% of PWH had a viral load <50 copies/mL, and 94% had a recent CD4 ≥200 cells/µL. The PWH group had a higher EAA, EEAA, GrimAge, and PhenoAge, and a lower DNAm-TL compared to the controls. IEAA was not different between groups. For PWH, there were significant negative correlations between IEAA and executive function, attention, and working memory and PhenoAge and attention. No associations between biomarkers and frailty were detected.

Conclusions

Evidence of epigenetic age acceleration was observed in AA older PWH using DNAm-based biomarkers of aging. There was no evidence of age acceleration independent of cell type National Institutes of Health composition (IEAA) associated with HIV, but this measure was associated with decreased cognitive function among PWH.
The Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission from Patients With Undiagnosed Coronavirus Disease 2019 (COVID-19) to Roommates in a Large Academic Medical Center
Authors: Karan Abraar , Klompas Michael , Tucker Robert , Baker Meghan , Vaidya Vineeta , Rhee Chanu
Published: June 2021

We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission between patients in shared rooms in an academic hospital between September 2020 and April 2021. In total, 11 290 patients were admitted to shared rooms, of whom 25 tested positive. Among 31 exposed roommates, 12 (39%) tested positive within 14 days. Transmission was associated with polymerase chain reaction (PCR) cycle thresholds ≤21.
Role of non-invasive multimodality imaging in autoimmune pericarditis
Authors: Jain Vardhmaan , Chhabra Garvit , Chetrit Michael , Bansal Agam , Berglund Felix , Montanè Bryce , Furqaan Muhammad M , Bachour Salaam P , Kontzias Apostolos , Forte Alexandra Villa , Aronow Wilbert S , Imazio Massimo , Cremer Paul C , Klein Allan L
Published: June 2021

Systemic autoimmune diseases are an important cause of pericardial involvement and contribute to up to ∼22% cases of pericarditis with a known aetiology. The underlying mechanism for pericardial involvement varies with each systemic disease and leads to a poor understanding of its management. Multimodality imaging establishes the diagnosis and determines the type and extent of pericardial involvement. In this review, we elaborate upon various pericardial syndromes associated with different systemic autoimmune and autoinflammatory diseases and the multitude of imaging modalities that can be used to further characterize autoimmune pericardial involvement. Lastly, these forms of pericarditis have a greater likelihood of recurrence, and clinicians need to understand their unique treatment approaches to improve patient outcomes.
Remote monitoring data from cardiac implantable electronic devices predicts all-cause mortality
Authors: Ahmed Fozia Zahir , Sammut-Powell Camilla , Kwok Chun Shing , Tay Tricia , Motwani Manish , Martin Glen P , Taylor Joanne K
Published: June 2021

Aims

To determine if remotely monitored physiological data from cardiac implantable electronic devices (CIEDs) can be used to identify patients at high risk of mortality.

Methods and results

This study evaluated whether a risk score based on CIED physiological data (Triage-Heart Failure Risk Status, ‘Triage-HFRS’, previously validated to predict heart failure (HF) events) can identify patients at high risk of death. Four hundred and thirty-nine adults with CIEDs were prospectively enrolled. Primary observed outcome was all-cause mortality (median follow-up: 702 days). Several physiological parameters [including heart rate profile, atrial fibrillation/tachycardia (AF/AT) burden, ventricular rate during AT/AF, physical activity, thoracic impedance, therapies for ventricular tachycardia/fibrillation] were continuously monitored by CIEDs and dynamically combined to produce a Triage-HFRS every 24 h. According to transmissions patients were categorized into ‘high-risk’ or ‘never high-risk’ groups. During follow-up, 285 patients (65%) had a high-risk episode and 60 patients (14%) died (50 in high-risk group; 10 in never high-risk group). Significantly more cardiovascular deaths were observed in the high-risk group, with mortality rates across groups of high vs. never-high 10.3% vs. <4.0%; P = 0.03. Experiencing any high-risk episode was associated with a substantially increased risk of death [odds ratio (OR): 3.07, 95% confidence interval (CI): 1.57–6.58, P = 0.002]. Furthermore, each high-risk episode ≥14 consecutive days was associated with increased odds of death (OR: 1.26, 95% CI: 1.06–1.48; P = 0.006).

Conclusion

Remote monitoring data from CIEDs can be used to identify patients at higher risk of all-cause mortality as well as HF events. Distinct from other prognostic scores, this approach is automated and continuously updated.
Montaigne’s Vagabond Styles: Political Homelessness in the Sixteenth Century
Authors: Claussen Emma
Published: June 2021

This article analyses political homelessness in French literature during the Wars of Religion (1562–1598), using Montaigne’s ‘De la vanité’ (‘Of Vanity’) as a case study. In that chapter, in which Montaigne discusses travel extensively, he aligns writers and vagabonds, later describing his writing style and way of thinking as vagabondage. There is no direct equivalent of the term ‘homelessness’ in early modern French, but ‘vagabond’ is frequently used to describe those of no fixed abode. Montaigne’s brief appropriations of the vagabond figure enable a reassessment of his relation to home and to politics, understood in the broader context of mass displacement and renewed philosophical reflection on home in this period. Firstly, the alignment between writers and vagabonds is read as a reference to Montaigne’s experience of papal censorship in Rome and an anticipation of his claim to be a citizen of the world. Montaigne’s creative vagabondage has affinities with Rosi Braidotti’s theory of ‘nomadic subjectivity’ (another kind of world-citizenship), which is both an aesthetic principle and a way of interrogating – and affirming – political agency. The article then goes on to analyse the extent to which Montaigne is ‘politically homeless’, in the sense that he is alienated by politics and refuses factionalism. Lastly, we consider Montaigne’s relation to homelessness in the context of contemporary print culture: the existence of clandestine ‘homeless texts’ reveals the limits of Montaigne’s strategic vagabondage. The conclusion then returns to the stakes of Montaigne’s claim that his style of writing is a ‘vagabond’ movement.
Unique patterns of mating pheromone presence and absence could result in the ambiguous sexual behaviors of Colletotrichum species
Authors: Wilson Andi M , Lelwala Ruvini V , Taylor Paul W J , Wingfield Michael J , Wingfield Brenda D
Published: June 2021

Colletotrichum species are known to engage in unique sexual behaviors that differ significantly from the mating strategies of other filamentous ascomycete species. For example, most ascomycete fungi require the expression of both the MAT1-1-1 and MAT1-2-1 genes to induce sexual reproduction. In contrast, all isolates of Colletotrichum harbor only the MAT1-2-1 gene and yet, are capable of recognizing suitable mating partners and producing sexual progeny. The molecular mechanisms contributing to mating types and behaviors in Colletotrichum are, however, unknown. A comparative genomics approach analyzing 35 genomes, representing 31 Colletotrichum species and two Verticillium species, was used to elucidate a putative molecular mechanism underlying the unique sexual behaviors observed in Colletotrichum species. The existence of only the MAT1-2 idiomorph was confirmed across all species included in this study. Comparisons of the loci harboring the two mating pheromones and their cognate receptors revealed interesting patterns of gene presence and absence. The results showed that these genes have been lost multiple, independent times over the evolutionary history of this genus. These losses indicate that the pheromone pathway no longer plays an active role in mating type determination, suggesting an undiscovered mechanism by which mating partner recognition is controlled in these species. This further suggests that there has been a redirection of the underlying genetic mechanisms that regulate sexual development in Colletotrichum species. This research thus provides a foundation from which further interrogation of this topic can take place.
Towards an open-source landscape for 3-D CSEM modelling
Authors: Werthmüller Dieter , Rochlitz Raphael , Castillo-Reyes Octavio , Heagy Lindsey
Published: June 2021

Large-scale modelling of 3-D controlled-source electromagnetic (CSEM) surveys used to be feasible only for large companies and research consortia. This has changed over the last few years, and today there exists a selection of different open-source codes available to everyone. Using four different codes in the Python ecosystem, we perform simulations for increasingly complex models in a shallow marine setting. We first verify the computed fields with semi-analytical solutions for a simple layered model. Then we validate the responses of a more complex block model by comparing results obtained from each code. Finally, we compare the responses of a real-world model with results from the industry. On the one hand, these validations show that the open-source codes are able to compute comparable CSEM responses for challenging, large-scale models. On the other hand, they show many general and method-dependent problems that need to be faced for obtaining accurate results. Our comparison includes finite-element and finite-volume codes using structured rectilinear and octree meshes as well as unstructured tetrahedral meshes. Accurate responses can be obtained independently of the chosen method and the chosen mesh type. The runtime and memory requirements vary greatly based on the choice of iterative or direct solvers. However, we have found that much more time was spent on designing the mesh and setting up the simulations than running the actual computation. The challenging task is, irrespective of the chosen code, to appropriately discretize the model. We provide three models, each with their corresponding discretization and responses of four codes, which can be used for validation of new and existing codes. The collaboration of four code maintainers trying to achieve the same task brought in the end all four codes a significant step further. This includes improved meshing and interpolation capabilities, resulting in shorter runtimes for the same accuracy. We hope that these results may be useful for the CSEM community at large and that we can build over time a suite of benchmarks that will help to increase the confidence in existing and new 3-D CSEM codes.