bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and testing of a steel regulating thermostatic valve
Authors: Antsiferov S A , Usmanova E A , Chirkova E V
Published: December 2019

A steel thermostatic valve group has been designed from a more affordable, cheaper domestic material - structural carbon steel grade PS08, which makes it possible to improve the manufacturability, installation, ease of the developed product operation, and reduce production costs. As a prototype, bronze thermostatic valves with threaded connections of foreign manufacturers were used, other geometrical parameters were determined by the production manufacturability. The results of the thermostatic valve steel body new design studies for two-pipe water heating systems are presented. A 3D model was built using the Solidworks design and graphics package, optimizing the geometric, mass, and strength valve characteristics. The application Solidworks Flow Simulation calculated the pressure loss in the digital 3D-model of the valve, its hydraulic characteristic was calculated. According to the numerical experiment results, a physical model of the valve group was manufactured and tested on a pouring stand. A comparison of the hydraulic characteristics of the digital and physical models was made, improvements to the design were made, and the purity of the internal surfaces was improved. A series of tests was carried out to determine the hydraulic characteristics for the regulating mechanism various values adjustment. In the heating season 2018 - 2019, full-scale tests were carried out at the operating facility with the installation of a valve and a thermal head on experimental convectors. The internal air average temperature measurements showed that the air temperatures in all the rooms with the same settings of the thermostatic head were within the acceptable limits. Therefore, the control quality of the pilot valve was adequate. The experimental thermostatic valve group was launched into small-scale production for the field tests in the buildings for various purposes.
Two-dimensional motion equations in water flow zone
Authors: Evtushenko S I , Kelekhsaev D B , Kokhanenko V N , Kondratenko A I
Published: December 2019

The paper studies a two-dimensional water flow from a non-pressure rectangular or round pipe placed into a wide horizontal channel. To simplify the problem, the real three-dimensional flow is modeled as a two-dimensional zone by eliminating the liquid particles’ velocities and accelerations in the direction perpendicular to the flow zone. To describe the water flow motion law, L. Euler’s equations for the ideal fluid are used, taking into account the continuity equations and the Bernoulli equation. The two-dimensional flow models in the spreading zone with the adequacy degree sufficient for practice, describe the movement of water flows arising in the lower road drainage systems races, Liman irrigation systems, small bridges, water volley channels, various culverts and water-crossing facilities. The obtained dependences of the velocity distribution, depth and water flow geometry give an accuracy exceeding that known by the previously used methods both by the velocity values and by the boundary current lines geometry.
A method for the identification of dynamic characteristics car suspension materials
Authors: Deryushev V , Zaitseva M , Megera G , Fedyanov A
Published: December 2019

Identification of dynamic characteristics of the machine suspension materials is required for troubleshooting and improving the ride quality. The method of identifying the suspension materials characteristics, based on the application of needle-shaped variation of the L.S. Pontryagin dynamical system to the invariant features of the dynamic system actual movement is presented in this study. The use of the needle-shaped parameters variation to the Hamilton-Ostrogradskyi action integral gives a condition of the objective functional minimum in the form of the maximum principle with the exception of the consideration of the vector of conjugate variables. As a result, the computational costs are reduced, the task of identification and optimization is simplified the convergence and accuracy of the algorithms is improved [1 - 5].
Traffic modeling
Authors: Kushchenko L E , Kushchenko S V , Baranov Y N , Dnistrenko N S
Published: December 2019

The transport infrastructure in the modern world is one of the most important infrastructures ensuring the life of regions and cities. Recently, in large cities, the possibilities of expanding transport networks have been exhausted. In this regard, special attention is paid to improving road safety, improving traffic management, optimal network planning and streamlining public transport routes. Solving these issues with minimal cost is possible with the help of traffic flow modeling [9].
The dynamic factor determination of the vibration mechanism with asymmetric vibrations
Authors: Gerasimov M , Vorobiov N , Romanovich M , Amini E
Published: December 2019

A vibration mechanism with asymmetric vibrations is discussed in the article. The mechanism consists of two stages of vibration blocks with directional vibrations. The asymmetric vibrations nature is estimated by the driving force components magnitude acting in opposite directions. The article deals with the obtaining rational parameters issue of a vibration mechanism with asymmetric vibrations, using the vibration mechanism dynamic factor. The vibration mechanism dynamic factor is numerically equal to the driving force largest component magnitude ratio to the smallest acting in the opposite direction. The work solves the following problems:

- obtaining the vibration mechanism dynamic factor maximum value with asymmetric oscillations at the driving force largest component given value;

- the conditions determination for reaching its maximum by the dynamic coefficient;

- the conditions determination for obtaining the total driving force maximum value of the vibration mechanism with asymmetric vibrations, consisting of several stages of vibrators with directional vibrations.
Special aspects of the use of “floating” cars information to estimate the quality of road traffic in real time
Authors: Topilin I , Zyryanov V , Volodina M
Published: December 2019

The article provides a rationale for the transition from the existing estimation methods of traffic conditions, focused on a single car-laboratory, to total "floating" cars methods of estimation at the network level. The paper presents the results of cluster and dispersion analyzes of experimental data. Based on these results it was concluded that a reliable estimation of the proportion of simultaneously stopped cars can be carried out when measuring traffic parameters with different time discreteness in the range from 1 to 180 seconds.
Multimodal transport as a mechanism for increasing the competition of long-distance passenger services
Authors: Kotenko Alexey , Malakhova Tatiana , Shchmanev Timofey
Published: December 2019

Multimodal transportation will not only increase the intensity of use of vehicles, but also reduce the passenger's travel time. The main task of organizing multimodal transportation is to maximally satisfy the demand of the population for transport services with the most efficient use of rolling stock. For a more effective solution to this problem, it is necessary to analyze the process of planning passenger transportation, evaluate the possibilities of marketing research in this area and conduct typifying of lines from the point of view of organizing multimodal transportation. The paper describes in detail the passenger transportation planning scheme and proposes an algorithm for assessing the effectiveness of managerial decisions. To improve the efficiency of making managerial decisions in the field of destination and cancellation of passenger trains of various categories, direct trains, trailing cars, organization of multimodal transportation, it is proposed to typify the lines with dividing them into 5 categories. Thus, the solution to the problem of maintaining the share of passenger traffic can be either the development of direct railway links, or the transition to multimodal transportation with the condition of coordinating the time of transfer.
New technology of the automated individual fuel consumption standardization for the motor vehicles
Authors: Moroz Sergey
Published: December 2019

A new technology of individual automated control of fuel consumption for the commercially operated motor vehicles is proposed. Thus, it allows the automatic collection of data on operating conditions, operating hours and fuel consumption of the vehicle. Moreover, this technology provides for the calculation of two packages of standards for a separate assessment of the technical condition of the vehicle and the quality of the driver’s work. Norms are unique for each motor vehicle and for each combination of the operating conditions and regimes. The new technology is going to minimize usage of motor vehicles with a high level of fuel consumption and provide an objective assessment of the driver’s quality and fuel efficiency for the commercially operated transport.
Method of complex organizational and technological designing underground structures and services
Authors: Oleynik Pavel
Published: December 2019

In the article it is considered a linkage of underground services construction sequence with buildings and constructions which allows imagining development model of entire underground space. For this purpose, it is proposed to divide the whole underground services into sections with their subsequent integration into homogeneous organizational and technological groups. Each of these groups has strictly defined erection sequence parameters in time schedule of facility construction. For the purpose of unification one developed organizational and technological solutions as rational schemes for above mentioned groups – schemes of temporary underground services functions replacement permanent, schemes of laying underground services under transport routes of construction site, etc.
Features of management of objects of protected areas of the Tyumen region
Authors: Bogdanova Olga , Varlamov Anatoly , Galchenko Svetlana
Published: December 2019

Tyumen region is a complex subject of the Russian Federation. Management of specially protected natural areas in this region has a number of features. In this article the example of legal contradiction and complexity of decision-making in cases of development of oil and gas fields and preservation of object of especially protected natural territories is considered.
The organization of transportations by container trains
Authors: Merkulina Irina , Kolesnik Georgiy , Kakhrimanova Diana , Ivanov Pavel , Saltakhanov Anzor
Published: December 2019

The article is devoted to the organization of transportation of container trains. The main elements of the transportation process and the main types of shipments are considered. Export railway deliveries from Russia to China began to develop relatively recently. China is actively purchasing Russian wood and wood materials, thereby raising the economic sector of the Russian Federation. The focus on the development of international rail transport is because with respect to other types of transport the railway is the most competitive. Transportation of large-sized various goods in large-capacity containers has a great prospect, both in the transport services sector and in foreign economic activity. Increasing such transportation means targeting the modernization of old rolling stock and the creation of new improved units to improve the efficiency and quality of cargo container traffic, as well as to reduce costs and shorten the delivery time for goods. To optimize both transit cargo and passenger, as well as import and export traffic, it is necessary to improve the border crossing procedure. Clearly, this issue requires discussion at the state and international levels, as well as the enormous costs of developing activities and the elimination of difficulties and time resources for the whole complex of procedures.
Study of the current state of the transport infrastructure of road and rail transport of the Russian Federation
Authors: Kurenkov Petr , Pokrovskaya Oksana , Anastasov Mark , Sokolov Mikhail , Bochkov Alexander
Published: December 2019

The transport system plays an important role in the conditions of dynamic development of the national economy, reliability and regularity of transport provision. The unified transport system is a combination of means of communication of conveyances, all types of transport, industrial enterprises, transport organizations, providing transportation of goods and passengers. This article describes the main advantages, disadvantages and specifics of railway transport. Currently, the majority of transport and economic land connections between the countries of Europe and Central, East and Southeast Asia to the territory of the Russian Federation, to its transport system, due to the peculiarities of the geographical position of the Russian Federation. The characteristic of the main Russian shipping companies is given. The main objects of the infrastructure of the railway industry in Russia. The main problems of the functioning of the railway industry of the Russian Federation listed. A comparative assessment of the railway transport network of Russia, USA, China and India is present. A SWOT analysis conducted to assess the strengths and weaknesses of the Russian rail and road transport.
Bridge health monitoring: the Davtashen bridge example in Yerevan
Authors: Sargsyan A N , Sargsyan G G , Sargsyan A A
Published: December 2019

AcceloAl system was developed by NUACA Chair of Roads and Bridges for the purpose of frequency-based bridges monitoring. The system allows measuring accelerations and determining the frequency of vibrations in real time, at four points of the bridge span simultaneously. The system provides the capability of making measurements both at the pier and the span. AcceloAl system has been used for monitoring of vibration frequency in the superstructure of Davtashen Bridge in Yerevan (Armenia). Davtashen Bridge has been chosen as a model for creating a Bridge Monitoring system for large bridges in Armenia. The results of the system usage and the analysis of measurements over the last years are presented in this paper.
Evaluation of reproduction processes and efficient operation of apartment blocks stock interrelation
Authors: Potapenko O S , Kuzovleva I A , Filippova T Ya
Published: December 2019

The article is dedicated to the interrelations analyzes of the reproduction processes in apartment blocks housing stock and efficiency indicators of housing operation in the region. Scientific novelty of the research is presented by the proposed system of criteria for assessing the reproduction and operation efficiency of housing, interaction modification diagram of housing stock markets and housing services.
Features of territorial organization of regional investment and construction complex in Russia
Authors: Khasheva I A , Serebryanaya D S , Serebryanaya I A , Sologub V A
Published: December 2019

Within the framework of the conducted comparative analysis, the features of the organization of the regional investment and construction complex were revealed; the dynamics of the construction industry was shown. Based on the in-depth analysis of the factors of formation and functioning of the investment and construction complex of the region, the question about identifying determinants of negative character was raised, the ways of improvement were offered.
Application of the engineering forecasting method in managing the competitiveness of a construction company
Authors: Pesotskaya E V , Selyutina L G , Egorova O A
Published: December 2019

The article discusses one of the pressing problems of managing a construction organization as a subject of the investment and construction market, focused on introducing new technologies and materials - the need to improve methods for assessing its competitiveness and making management decisions to ensure, maintain and develop the competitiveness in strategic and tactical periods. An algorithm for assessing the competitiveness of a construction organization based on the integration of particular indicators characterizing competitiveness, taking into account the significance and intensity of their determining effect is presented. The algorithm is formed on the basis of an engineering forecasting methodology intended for solving comparison and multi-criteria tasks. The necessity and possibility of using an expert method in assessing the competitiveness of a construction organization, requirements for the procedure for its application, as well as a methodical approach to the implementation of monitoring of the competitive environment of the investment and construction market are revealed.
The construction materials actual cost accounting issues in terms of the estimated and regulatory framework reforming
Authors: Golikova U A , Voronova S P , Narkevskaya T V , Shaikina L K
Published: December 2019

Some problems in the materials actual cost accounting caused by the operating methodological and regulatory framework imperfection and discrepancy in the conditions of pricing system reforming and budget rationing in construction are considered in this article. These problems’ influence on the receipt accounting processes and the construction materials use is discussed.
Informational platform of the digital accounting
Authors: Shumeyko M V , Sagamonova G V , Sagamonova E V
Published: December 2019

The article discusses the background and the need for transition to digital technologies in the economy at the global, macro, meso and micro levels. The necessary and sufficient conditions for creating a microeconomic platform for digital accounting are analyzed. The complex of problems of their creation and the ways of their solution are investigated.
Development of protective measures providing environmental safety in areas affected by water-intake constructions of urban households
Authors: Bondarenko V L , Khetsuriani E.D. , Ilyasov A.I. , Semenova E.A.
Published: December 2019

The article represents the results of integrated studies of development of protective measures providing environmental safety in areas affected by water-intake technological complexes as a technological component of specified type of natural-technical systems (NTS) ‘natural aqueous medium – water intake technological complex – multiple-use water supply system’ (NAS-WITC-MUSS) concerned with a stable residential water supply of urban households.
Calculation of an electrochemical reactor for cleaning the air of the city from hydrogen sulfide emissions
Authors: Golovanchikov A. , Churikova V. , Fomichev V.
Published: December 2019

The environmental safety of the urban economy requires the creation of new environmentally friendly technologies that ensure human protection from the negative impact of water management systems, in particular the urban sewer system, which is a potentially dangerous source of decomposition products of biological waste. Hydrogen sulfide is a gas that has a significant danger for both the city population and the high corrosivity of metal and concrete structures. At the Department of General and Applied Chemistry (VSTU), we developed an electrochemical method for purifying air from hydrogen sulfide, which allows to neutralize it locally, in the zone of hydrogen sulfide emission, with the release of environmentally friendly products: chemically pure sulfur and water.
Comparison of sulfin hydrogen cleaning processes in a gas mixture in a packed adsorporal and electrochemical reactors
Authors: Golovanchikov A B , Churikova V I , Fomichev V T
Published: December 2019

In this article given a comparative economic and environmental calculation of the use of a packed absorption column and an electrochemical reactor designed to purify air of hydrogen sulfide in the processes of ensuring environmental safety from potentially negative impacts of the surrounding technical facilities of the city, accompanied by emissions of hydrogen sulfide generated in sewers and emitted into the air of settlements. A significant advantage of the electrochemical air purification from hydrogen sulfide is shown compared with the absorption method of cleaning in packed columns using an aqueous solution of monoethanolamine as an absorbent. On the basis of practical experimental data, the optimal technological parameters of the process of electrochemical oxidation of hydrogen sulfide (current and voltage values) and the circuit diagram of a flow-through electrochemical reactor are determined.
Ensuring the protection of the environment at the combined feed mills
Authors: Belova T I , Agaskov E M , Chernova E G , Terekhov S V
Published: December 2019

There is a great amount of technological lines producing the combine feed of various compositions, forms and consistency, what dramatically effects on the condition of the environment; during the process of its producing the significant emission of the plant- and mineral-based dust happens; that is why the development of the complex of the systemic events “dust-removal - dedusting” is so significant. The article is devoted to one of the elements of this system – the process of the dust removal. The projected system as well as the laboratory facility for studying the effectiveness of the aforementioned system, and the results of the laboratory experiments allow to low the dust emission at the combined feed mills.
Monitoring the dispersed composition of dust particles on the leaf blades of common lilac (Syringa vulgaris), small-leaved elm (Ulmus parvifolia), common apricot (Prunus armenica) in urban agglomeration
Authors: Glinyanova Irina , Azarov Valery
Published: December 2019

The article presents the study results of dusty particles on the leaves of tree species forms in the residential area of the Sredneahtubinsky district of the Volgograd region. The aim of the study was to monitor the dispersed composition of dust particles on various types of urban vegetation. Leaves of common lilac (Syringa vulgaris), small-leaved elm (Ulmus parvifolia), common apricot (Prunus armenica) as mass plant species growing in the residential area of the Sredneahtubinsky district of the Volgograd region were chosen as objects of study. The novelty of the work is the study dispersed composition of dust particles on the leaves of common lilac (Syringa vulgaris), small-leaved elm (Ulmus parvifolia), common apricot (Prunus armenica) from the standpoint of random functions expressed by integral distribution curves of particle mass over their equivalent diameters. The measurement of dust particles, dust processing, and the study of dust dispersed composition of was carried out in accordance with GOST R 56929-2016 using the SPOTEXPLORER computer program. As a result of the studies, it was found that the surface of the laminate leaf of common lilac (Syringa vulgaris) and elm have the best adsorption ability small-leaved (Ulmus parvifolia). The study's results are of practical importance - they provide information on the urban plants ability of leaves surface to retain fine-dispersed dust, offer a specific range of plant species for urban green areas, which can use the regional public services greening of urban areas in order to reduce PM2.5 emissions of PM10 in urban areas.
High porosity micro- and macro-cellular copper foams with semi-open cell microstructure toward its physical and mechanical properties
Authors: Saberi Yasaman , Oveisi Hamid
Published: December 2019

Herein, a powder compacting method was developed to fabricate high porosity micro- and macro-cellular copper foams using CaCO3 space holder. The cold compacted precursors were heated at different temperatures under the nitrogen atmosphere. The effects of precursor compaction pressure, space holder content and sintering temperature on cell microstructure, relative density, compressive and physical properties were investigated. The scanning electron microscopy (SEM) images showed a uniform distribution of interconnected pores with sizes of pores and channels less than 50 microns formed the semi-open cell structure of the fabricated foams. The evaluation of the foaming agent content, 0 to 20 (wt%), in precursor materials showed relatively large changes in the porosity percentage (27%–50%), with the utilitarian strength (43 MPa) and densification strain (40%) of the copper foams. For specimens having 20 wt% CaCO3, tuning the sintering temperature (600 °C) and compacting pressure (500 MPa) of precursors tailored superior porosity percent (47%), remarkable compressive stress (501 MPa) and high thermal (43.8 W m−1.k), and electrical conductivity (0.06 × 10 8 Ω−1 m−1) owing to a desirable foaming process. A massive gas release during the CaCO3 decomposition and the strengthened cell walls of the copper foams during the sintering resulted in the high porosity and strength of the fabricated foams. The presented fabrication method and our results are the core elements for the development of new high porosity metal foams that can help the development of the future application of copper foams for a long-life anode for lithium-ion batteries, catalysis, and thermal and electrical performances as electronic cooling materials.
Nanoparticles for organic electronics applications
Authors: He Zhengran , Zhang Ziyang , Bi Sheng
Published: December 2019

Recently, the research in solution-based, small-molecule organic semiconductors has achieved great progress, although their application in organic electronics devices is still restricted by a variety of issues, including crystal misorientation, morphological nonuniformity and low charge-carrier mobility. In order to overcome these issues, hybrid material systems that incorporate both organic semiconductors and additives have been successfully demonstrated to control crystal growth and charge transport of the organic semiconductors. In this work, we first review the recent advances in the charge-carrier mobility of the organic semiconductors, followed by a comparison of the different additives that have been reportedly blended with the semiconductors, including polymeric additives, small-molecule additives and nanoparticle based additives. Then we will review the important nanoparticles employed as additives to blend with solution-based, organic semiconductors, which effectively improved the semiconductor crystallization, enhanced film uniformity and increased charge transport. By discussing specific examples of various well-known organic semiconductors such as 6, 13-bis (triisopropylsilylethynyl) pentacene (TIPS pentacene), we demonstrate the essential relationship among the crystal growth, semiconductor morphology, dielectric properties, and charge-carrier mobilities. This work sheds light on the implementation of nanoparticle additives in high-performance organic electronics device application.
Spatial heterogeneity of climate variation and vegetation response for Arctic and high-elevation regions from 2001–2018
Authors: Wu Wenjin , Sun Xiaohui , Epstein Howard , Xu Xiyan , Li Xinwu
Published: December 2019

In recent decades, an amplification of warming in Arctic and high-elevation regions has been widely observed, along with a general enhancement of vegetation growth. However, driven by variability in controlling factors and complex mechanisms, climate and vegetation changes can be highly heterogeneous in space and time. In this study, an analysis is performed separating Arctic and Tibetan Plateau (TP) vegetated areas into various units according to a map of terrestrial ecoregions. The most recent variations of heat, moisture, and vegetation growth (MODIS Normalized Difference Vegetation Index) are evaluated over 2001–2018. Relationships among the climate and vegetation variables are assessed. Six distinct change patterns are identified: (1) synchronized increase of day and night temperature and precipitation during April to October coinciding with strong vegetation greening, (2) profound warming with no change in precipitation and vegetation, (3) an increase of summer temperature and vegetation with a negative latitudinal gradient, (4) greening under increased precipitation without warming, (5) browning not likely being driven by climate, (6) warming only during the nighttime and moderately enhanced vegetation growth. It is demonstrated that vegetation growth in the Arctic and TP is largely controlled by nighttime temperature and precipitation, as opposed to daytime temperature. The exception is the Canadian Arctic, where greening is directly related to summer daytime warming, and a contrasting relationship is observed on the TP. The underlying causes of these patterns are discussed, relating them to multiple mechanisms reported in the literature. These findings may help to further understand the changing Arctic and high-elevation climate and its effects on vegetation growth.
The nonlinear stability regime of the viscous Faraday wave problem
Authors: Altizio David , Tice Ian , Wu Xinyu , Yasuda Taisuke
Published: December 2019

This paper concerns the dynamics of a layer of incompressible viscous fluid lying above a vertically oscillating rigid plane and with an upper boundary given by a free surface. We consider the problem with gravity and surface tension for horizontally periodic flows. This problem gives rise to flat but vertically oscillating equilibrium solutions, and the main thrust of this paper is to study the asymptotic stability of these equilibria in certain parameter regimes. We prove that both with and without surface tension there exists a parameter regime in which sufficiently small perturbations of the equilibrium at time

t
=
0

t = 0

give rise to global-in-time solutions that decay to equilibrium at an identified quantitative rate.
Unpacking Parental Violence in Narratives: Agency, Guilt, and Pedagogy in Narratives about Traumatic Interpersonal Experiences
Authors: Deppermann Arnulf
Published: December 2019

This article deals with narratives of traumatic experiences of parental violence in childhood, told by adult narrators in the context of clinical adult attachment interviews. The study rests on a corpus of interviews with 20 patients suffering from fibromyalgia, who were interviewed in the context of psychodynamic psychotherapy. Nine of the patients reported repeated experiences of parental violence. The article focuses on extracts from two interviews, which provide for a maximal contrast concerning the practices of telling experiences of violence and which are ‘clear cases’ of the practices that are characteristic of the whole corpus. The main differences between the different ways of telling concern:

• With respect to the ascription of guilt and responsibility, parental violence is portrayed as legitimate pedagogic action versus as being evil-minded and guilty without rational justification.

• With respect to the process of the telling, we find narrative trajectories over which an initial vague gloss is increasingly unpacked by reports of highly violent actions versus narratives in which violence is overtly stated and morally ascribed from its very first mention.
Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation
Authors: Hutchison Luke A D , Berger Bonnie , Kohane Isaac S
Published: December 2019

Motivation

The advent of in vivo automated techniques for single-cell lineaging, sequencing and analysis of gene expression has begun to dramatically increase our understanding of organismal development. We applied novel meta-analysis and visualization techniques to the EPIC single-cell-resolution developmental gene expression dataset for Caenorhabditis elegans from Bao, Murray, Waterston et al. to gain insights into regulatory mechanisms governing the timing of development.

Results

Our meta-analysis of the EPIC dataset revealed that a simple linear combination of the expression levels of the developmental genes is strongly correlated with the developmental age of the organism, irrespective of the cell division rate of different cell lineages. We uncovered a pattern of collective sinusoidal oscillation in gene activation, in multiple dominant frequencies and in multiple orthogonal axes of gene expression, pointing to the existence of a coordinated, multi-frequency global timing mechanism. We developed a novel method based on Fisher’s Discriminant Analysis to identify gene expression weightings that maximally separate traits of interest, and found that remarkably, simple linear gene expression weightings are capable of producing sinusoidal oscillations of any frequency and phase, adding to the growing body of evidence that oscillatory mechanisms likely play an important role in the timing of development. We cross-linked EPIC with gene ontology and anatomy ontology terms, employing Fisher’s Discriminant Analysis methods to identify previously unknown positive and negative genetic contributions to developmental processes and cell phenotypes. This meta-analysis demonstrates new evidence for direct linear and/or sinusoidal mechanisms regulating the timing of development. We uncovered a number of previously unknown positive and negative correlations between developmental genes and developmental processes or cell phenotypes. Our results highlight both the continued relevance of the EPIC technique, and the value of meta-analysis of previously published results. The presented analysis and visualization techniques are broadly applicable across developmental and systems biology.

Availability and implementation

Analysis software available upon request.

Supplementary information

Supplementary data are available at Bioinformatics online.
A haplotype-awarede novoassembly of related individuals using pedigree sequence graph
Authors: Garg Shilpa , Aach John , Li Heng , Sebenius Isaac , Durbin Richard , Church George
Published: December 2019

Motivation

Reconstructing high-quality haplotype-resolved assemblies for related individuals has important applications in Mendelian diseases and population genomics. Through major genomics sequencing efforts such as the Personal Genome Project, the Vertebrate Genome Project (VGP) and the Genome in a Bottle project (GIAB), a variety of sequencing datasets from trios of diploid genomes are becoming available. Current trio assembly approaches are not designed to incorporate long- and short-read data from mother–father–child trios, and therefore require relatively high coverages of costly long-read data to produce high-quality assemblies. Thus, building a trio-aware assembler capable of producing accurate and chromosomal-scale diploid genomes of all individuals in a pedigree, while being cost-effective in terms of sequencing costs, is a pressing need of the genomics community.

Results

We present a novel pedigree sequence graph based approach to diploid assembly using accurate Illumina data and long-read Pacific Biosciences (PacBio) data from all related individuals, thereby generalizing our previous work on single individuals. We demonstrate the effectiveness of our pedigree approach on a simulated trio of pseudo-diploid yeast genomes with different heterozygosity rates, and real data from human chromosome. We show that we require as little as 30× coverage Illumina data and 15× PacBio data from each individual in a trio to generate chromosomal-scale phased assemblies. Additionally, we show that we can detect and phase variants from generated phased assemblies.

Availability and implementation

https://github.com/shilpagarg/WHdenovo.
Detection of natural hybridization and delimitation of two closely related operational taxonomic units of the Astyanax fasciatus (Teleostei: Characidae) complex through integrative approaches
Authors: Gavazzoni Mariane , Pavanelli Carla S , Graça Weferson J , Melo Bruno F , Gubiani Éder André , Margarido Vladimir P
Published: December 2019

Astyanax is a species-rich, non-monophyletic genus composed of several supraspecific taxa that are poorly delimited. The Astyanax fasciatus complex is one of these taxa and shows high taxonomic complexity. To elucidate the evolutionary history of the A. fasciatus complex from southern South America, we conducted cytogenetic, molecular and morphological analyses in specimens from the Uruguay River basin. Cytogenetic characters demonstrated two closely related operational taxonomic units: Astyanax sp. 1 (8m+22sm+10st+6a), Astyanax sp. 2 (8m+24sm+10st+4a) and natural hybrids (8m+23sm+8st+5a). 5S ribosomal DNA sites were found in two pairs of m chromosomes and one pair of a chromosomes in Astyanax sp. 1, two pairs of a chromosomes and one pair of m chromosomes in Astyanax sp. 2, and three m chromosomes and three a chromosomes in hybrids. As51 sites were found in three chromosomes in Astyanax sp. 1 and in five chromosomes in Astyanax sp. 2 and hybrids. Mitochondrial sequence analyses did not separate the two units and hybrids. Morphological analyses revealed differences between Astyanax sp. 2 and hybrids. This secondary contact with gene flow between lineages that diverged long ago might slow or reverse the differentiation/speciation process. These results help us to understand the evolutionary history of this highly complex clade of Astyanax in southern South America.
Historical biogeography and multi-trait evolution in miniature toadlets of the genus Brachycephalus (Anura: Brachycephalidae)
Authors: Condez Thais H , Haddad Célio F B , Zamudio Kelly R
Published: December 2019

Evolutionary changes towards a miniaturized body plan may directly affect other important phenotypic traits related to the physiology, behaviour and ecology of organisms. The frog genus Brachycephalus is an outstanding example of a radiation of miniaturized species endemic to the Brazilian Atlantic Forest. We inferred ancestral states and historical changes in body size, body colour and hyperossification to test hypotheses about diversification and selective environmental mechanisms leading to the evolution of these specialized traits. The ancestral distribution was associated with high-elevation regions in the northern Serra do Mar mountain range, and diversification in the genus was coincident with important geological and climatic events during the history of the Atlantic Forest. The dynamic historical changes provided an opportunity for multiple lowland lineages and for speciation via dispersal and vicariance in multiple invasions of the highlands. The ancestral Brachycephalus was reconstructed as miniaturized and dull coloured, without hyperossification in the skin, skull or postcranial skeleton. A parallel evolution of phenotypic traits has occurred in northern and southern Atlantic Forest lineages, beginning in the Miocene. Shifts in body size are not related to elevation range or latitude. However, we found a significant correlation between the evolution of hyperossification and aposematism with increasing body size.
Trans-ethnic meta-analysis of rare variants in sequencing association studies
Authors: Shi Jingchunzi , Boehnke Michael , Lee Seunggeun
Published: December 2019

Trans-ethnic meta-analysis is a powerful tool for detecting novel loci in genetic association studies. However, in the presence of heterogeneity among different populations, existing gene-/region-based rare variants meta-analysis methods may be unsatisfactory because they do not consider genetic similarity or dissimilarity among different populations. In response, we propose a score test under the modified random effects model for gene-/region-based rare variants associations. We adapt the kernel regression framework to construct the model and incorporate genetic similarities across populations into modeling the heterogeneity structure of the genetic effect coefficients. We use a resampling-based copula method to approximate asymptotic distribution of the test statistic, enabling efficient estimation of p-values. Simulation studies show that our proposed method controls type I error rates and increases power over existing approaches in the presence of heterogeneity. We illustrate our method by analyzing T2D-GENES consortium exome sequence data to explore rare variant associations with several traits.
Heterologous Antibody Responses Conferred by A(H3N2) Variant and Seasonal Influenza Vaccination Against Newly Emerged 2016–2018 A(H3N2) Variant Viruses in Healthy Persons
Authors: Liu Feng , Levine Min Z
Published: December 2019

Background

Swine origin A(H3N2) variant [A(H3N2)v] viruses continue to evolve and remain a public health threat. Recent outbreaks in humans in 2016–2018 were caused by a newly emerged A(H3N2)v cluster 2010.1, which are genetically and antigenically distinct from the previously predominant cluster IV. To address the public health risk, we evaluated the levels of heterologous cross-reactive antibodies to A(H3N2)v cluster 2010.1 viruses induced from an existing cluster IV A(H3N2)v vaccine and several seasonal inactivated influenza vaccines (IIVs) in adults, elderly individuals, and children.

Methods

Human vaccine sera and ferret antisera were analyzed by hemagglutination inhibition (HI) and neutralization assays against representative A(H3N2)v viruses from clusters IV and 2010.1 and seasonal A(H3N2) viruses.

Results

Ferret antisera detected no or little cross-reactivity between the 2 A(H3N2)v clusters or between A(H3N2)v and seasonal A(H3N2) viruses. In humans, cluster IV A(H3N2)v vaccine induced antibodies cross-reactive to cluster 2010.1 viruses in approximately one-third of the 89 adult and elderly vaccinees. Seasonal IIVs did not induce seroprotective antibodies (≥40) to A(H3N2)v viruses in young children, but induced higher antibodies to A(H3N2)v viruses in cluster 2010.1 than those in cluster IV in adults.

Conclusions

Cluster IV A(H3N2)v vaccine did not provide sufficient heterologous antibody responses against the new 2010.1 cluster A(H3N2)v viruses. Seasonal IIV could not induce seroprotective antibodies to 2010.1 cluster A(H3N2)v viruses in young children, suggesting that young children are still at high risk to the newly emerged A(H3N2)v viruses. Continued surveillance on A(H3N2)v viruses is critical for risk assessment and pandemic preparedness.
A species of magnetotactic deltaproteobacterium was detected at the highest abundance during an algal bloom
Authors: Pan Hongmiao , Dong Yi , Teng Zhaojie , Li Jinhua , Zhang Wenyan , Xiao Tian , Wu Long-Fei
Published: December 2019

Magnetotactic bacteria (MTB) are a group of microorganisms that have the ability to synthesize intracellular magnetic crystals (magnetosomes). They prefer microaerobic or anaerobic aquatic sediments. Thus, there is growing interest in their ecological roles in various habitats. In this study we found co-occurrence of a large rod-shaped deltaproteobacterial magnetotactic bacterium (tentatively named LR-1) in the sediment of a brackish lagoon with algal bloom. Electron microscopy observations showed that they were ovoid to slightly curved rods having a mean length of 6.3 ± 1.1 μm and a mean width of 4.1 ± 0.4 μm. Each cell had a single polar flagellum. They contained hundreds of bullet-shaped intracellular magnetite magnetosomes. Phylogenetic analysis revealed that they were most closely related to Desulfamplus magnetovallimortis strain BW-1, and belonged to the Deltaproteobacteria. Our findings indicate that LR-1 may be a new species of MTB. We propose that deltaproteobacterial MTB may play an important role in iron cycling and so may represent a reservoir of iron, and be an indicator species for monitoring algal blooms in such eutrophic ecosystems. These observations provide new clues to the cultivation of magnetotactic Deltaproteobacteria and the control of algal blooms, although further studies are needed.
Responsible Science and Research Animal Use
Authors: Turner Patricia V , Barbee R Wayne
Published: December 2019

This issue of the ILAR Journal focuses on the topic of responsible science as it relates to animal research. We start with the concept of the scientist as a responsible citizen and then move through multiple phases of research including careful experimental planning, reporting, and incorporation of laboratory animal science. The work of the Institutional Animal Care and Use Committee (IACUC) or animal ethical/oversight body in reviewing both animal use and contributing to scientific excellence is explored. Additional topics include protection of animal handlers from multiple experimental hazards, use of agricultural animals and wildlife studies, regulatory ambiguities, and harmonization of animal research. Rounding out the issue is a discussion of how animal care and use programs can enhance animal welfare while mitigating regulatory burden, and our responsibility to clearly communicate the ethical use of animals in advancing biomedical research. A deeper understanding of these topics can assist scientists in simultaneously advancing their research and animal welfare.
Persistence of Immune Responses With an Inactivated Japanese Encephalitis Single-Dose Vaccine, JENVAC and Interchangeability With a Live-Attenuated Vaccine
Authors: Vadrevu Krishna Mohan , Potula Venugopal , Khalatkar Vasant , Mahantshetty Niranjana S , Shah Atish , Ella Raches
Published: December 2019

Background

This study reports immunogenicity, safety, and interchangeability of a single-dose, inactivated, Vero-cell derived, JENVAC to the live-attenuated SA 14-14-2 vaccine in healthy children.

Methods

This phase 4, multicenter, open-label, randomized, control trial enrolled 360 children who were equally randomized to receive a single dose of either JENVAC or SA 14-14-2. Children were followed at various time points, until 2 years (day 720) postvaccination, upon which a subset from each group was divided and allocated to a receive a booster dose or the other vaccine.

Results

At all time points, immunological measures were statistically higher in the JENVAC group. In the interchangeability study, children receiving 2 doses of JENVAC reported significantly higher response compared with 2 doses of SA 14-14-2. No difference in adverse events was observed. These corroborate with excellent seroprotection after the first dose of an earlier JENVAC study.

Conclusions

A single-dose vaccination with JENVAC induces protective titers that persist up to 1 year. We report appreciable interchangeability between both vaccines, with JENVAC/JENVAC combination exhibiting the highest immune response. JENVAC is now licensed as a single-dose Japanese encephalitis vaccine.
Federal and State Action Needed to End the Infectious Complications of Illicit Drug Use in the United States: IDSA and HIVMA’s Advocacy Agenda
Authors: Springer Sandra A , Barocas Joshua A , Wurcel Alysse , Nijhawan Ank , Thakarar Kinna , Lynfield Ruth , Hurley Hermione , Snowden Jessica , Thornton Alice , del Rio Carlos
Published: December 2019

In response to the opioid crisis, IDSA and HIVMA established a working group to drive an evidence- and human rights-based response to illicit drug use and associated infectious diseases. Infectious diseases and HIV physicians have an opportunity to intervene, addressing both conditions. IDSA and HIVMA have developed a policy agenda highlighting evidence-based practices that need further dissemination. This paper reviews (1) programs most relevant to infectious diseases in the 2018 SUPPORT Act; (2) opportunities offered by the “End the HIV Epidemic” initiative; and (3) policy changes necessary to affect the trajectory of the opioid epidemic and associated infections. Issues addressed include leveraging harm reduction tools and improving integrated prevention and treatment services for the infectious diseases and substance use disorder care continuum. By strengthening collaborations between infectious diseases and addiction specialists, including increasing training in substance use disorder treatment among infectious diseases and addiction specialists, we can decrease morbidity and mortality associated with these overlapping epidemics.