bluuebunny/crossref_metadata_2025 huggingface dataset:
V International scientific and practical conference “Actual problems of the energy complex: physical processes, mining, production, transmission, processing and environmental protection” (APEC-V-2022)
Authors: Sadullozoda Shahriyor , Uzakov Gulom , Gibadullin Arthur
Published: August 2022

The presented material is devoted to the results of the V International scientific and practical conference “Actual problems of the energy complex: physical processes, mining, production, transmission, processing and environmental protection” (APEC-V-2022).

List of International Program Committee are available in this pdf.
Analysis of electricity consumption of electrical machines of a coal industry enterprise using the wavelet transform
Authors: Manusov V Z , Orlov D V , Sultonov Sherkhon , Ahyoev Javod , Bumtsend Uyangasaikhan
Published: August 2022

The priority directions of the prospective development of the energy sector involve improving the quality of generated electricity, reducing the consumption of fuel resources, and implementing modern technologies and methodologies. These strategies are considerably aimed at enterprises of the fuel and energy sector having individual features of electricity consumption. Predictive control of technological processes of these objects is a relevant problem that, in turn, requires the use of up-to-date methods of data analysis and processing. One of these methods is the wavelet transform having several advantages over known methods, such as the Fourier transform. The paper presents a comparative analysis of the wavelet transform of active power consumption for various excavators of a mining enterprise in the Siberian region. The obtained results illustrate the statistics of operation of each excavator and allow making conclusions about their operation for a chosen time interval and presenting them in the form of a 3D model. Mathematical instruments of wavelet analysis can be introduced into existing complexes of automated control systems for the production process of enterprises. The proposed method indicates the possibility of developing the predictive control in the electricity consumption process, planning price categories and optimizing the load schedule with cost reduction and an increase of the financial profit of the enterprise.
Energy saving and energy efficiency improvement in the Russian Federation
Authors: Chernykh A G , Barykina Y N , Shao Yuwen
Published: August 2022

The article emphasizes the need for developing and implementing energy-saving technologies to improve energy efficiency. Technological terms used in the process of energy saving are defined. The system of energy saving and energy efficiency improvement as an integral part of the federal energy policy of Russia is described taking into account the development of various industries. The current trends in the regulation of relations in this area are analyzed. The article describes energy-saving technologies that can be used by industrial enterprises. Based on the world and Russian practices, organizational measures in the field of energy saving and energy efficiency are suggested.
Population dynamics of forest-forming tree species on landslide-scree slopes of the right bank of the Kuibyshev reservoir (Tatarstan)
Authors: Kotova N A , Fardeeva M B , Usmanov B M
Published: August 2022

The dynamics of forest-forming tree populations under conditions of landslide slopes makes it possible to assess the impact and the anthropogenic regulation of the Kuibyshev reservoir on the forest vegetation state. The Shannon index characterizes the phanerophytes diversity in the structure of forests by landslide elements. The integral signs of the activity/stability of landslide processes on the slopes are the trees functional parameters – the trunks height, the dynamics of cross-sectional areas and wood volumes, reflecting not only the different trees populations state and productivity according to the landslide elements, but also the stage of phytocenoses reforestation of along the right bank of the Kuibyshev reservoir.
Modeling and research of power supply systems with renewable energy sources and hydrogen fuel cells
Authors: Marchenko O V , Podkovalnikov S V , Solomin S V
Published: August 2022

Currently, the creation of environmentally friendly energy systems, including only renewable energy sources, is an urgent task. In this paper, such an autonomous power supply system (microgrid) for isolated consumers is investigated. It includes photovoltaic converters, wind turbines, an electrolyzer, fuel cells, electrical energy and hydrogen storage. For its study, an original optimization mathematical model was used. The optimal structure of the system and its operation modes are determined according to the criterion of minimum total discounted costs, taking into account energy balances and a number of additional conditions and constrains. It is shown that the use of energy sources of various types and energy storage devices makes it possible to smooth out the uneven generation of solar and wind power plants. It has been established that it is expedient to use electric batteries for short-term, and hydrogen accumulators – for long-term energy storage.
Methodological toolkit for assessing the impact of renewable energy on the balanced development and preservation of the regional carbon cycle
Authors: Dvinin D , Davankov A , Plaksina A
Published: August 2022

The article provides methodological tools that allow to carry out a socio-ecological and economic assessment of the balance of regions in the development of renewable (alternative) energy sources. When forecasting the development of renewable energy in the region, it was taken into account that, unlike fossil fuel-based energy, it does not have a significant impact on the environment, since it uses material and energy flows circulating in natural systems. During the study, it was found that only one transition to renewable energy sources will not allow achieving carbon balance in the regions. The landscape features of the region significantly affect the possibility of its conservation. Therefore, in each region, it will be necessary to identify the area of territories with a special nature conservation status that will allow maintaining the carbon cycle. Methodological tools were tested on the example of the Chelyabinsk region of the Russian Federation. As a result, it was found to maintain a balanced carbon cycle, it will be necessary to increase the share of natural steppes to 49.1% of the total area of the region, and achieve the value of renewable energy in the regional energy balance up to 93%.
Multicriteria investigation of the efficiency of combining a NPP power unit with a heat storage system
Authors: Aminov R Z , Yurin V E
Published: August 2022

A heat storage system, including an additional low-power steam turbine, can provide effective participation of nuclear power plants in covering daily irregularities in energy consumption in the power system. In addition, the system provides an additional reserve for the NPP’s own needs, due to the possibility of using the energy of residual heat release from the reactor core to supply power to the station’s own needs. In the paper, the methodology developed by the authors is presented, which allows to research ways to improve the efficiency of nuclear power plants based on a comprehensive assessment of technical and economic efficiency, changes in plant safety and effects for the entire state energy system as a whole, achieved through the installation of new equipment. As an example, a thermal storage system, a steam-gas plant, and a system for passive heat removal from the reactor core have been investigated.
Removal of hydrodynamic lesions of a heated floor with a solar collector
Authors: Khamraev S I , Kh Ibragimov U , Kamolov B I
Published: August 2022

This paper presents the results of an experimental study of the hydrodynamic process of a solar collector water-heated floor system. The water-heated floor system is designed to heat living rooms. Based on the analysis of the structures of the hot water floor, methods of their installation and the methodology of hydrodynamic calculation of the hot floor, experimental studies were conducted on the total pressure loss in the pipes of the hot water floor and the pump power used to transfer hot water from the pipes. Experimental studies were carried out in laminar and turbulent flow regimes at different diameters and different positioning steps of the water-heated floor pipe. The results of the hydrodynamic process study showed that the pressure drop and pump power were the highest at the pipe diameter and pipe pitch of 12 mm and 100 mm, i.e. 8 kPa and 18.5 W in the laminar mode and 14 kPa and 210 W in the turbulent mode. . Results obtained as the pressure loss and the power consumption of the pump decrease with increasing pipe diameter and positioning pitch ΔP = f(Re) and N = f(Re) presented in the form of a dependency graph.
Concerning prognostic estimations on hazardous weather events: a road to nowhere or to home?
Authors: Kolokolov Yu , Monovskaya A
Published: August 2022

Changes of local climate dynamics influence on the demand of fuel-energy facilities and on the choice of priorities of the most promising technological processes of production and transportation of fuel-energy resources. The corresponding adjustment is quite inertial, so, it is a point of the long-term strategy of development of a fuel and energy complex. Meantime, manipulations of a public opinion regarding the climate change problems occurs due to an audience prefers to remain within habitual empirical considerations and to listen to bright media talkers skillfully juggling various futuristic conclusions about the climate instead of accurate-but-tedious scientific proofs demanding sufficient interdisciplinary training and careful verifications by real physical data. The paper cautions about extremely dangerous harvests of unexampled climate-related damages that are grown soon on such fruitful populist fields. The paper notes substitutions of purposes by tools and demonstrates in what extent traditional estimations on climate-related hazards can be far from the real ones because of many potentialities of local climate changes are originally latent from the scope of the dominating concept on “averaging” climate norms. The paper will be interesting to responsible researchers, practitioners and citizenry oriented to efficient work to hold back from the transition towards the destructive-for-human-activities novel global climate.
Method for determining the sizes of structural elements and semi-empirical formula of thermal characteristics of solar dryers
Authors: Mirzaev Sh , Kodirov J , Khamraev S I
Published: August 2022

By choosing the initial dimensions of flat solar collectors, and by measuring the temperature of the incoming and outgoing air from the collector, it is possible to determine the linear dimensions of the drying cabinet attached to the collector. It is also possible to establish the basic semi-empirical formulas for determining the thermal characteristics of solar dryers. This calculation method was applied to design and build a study of an indirect solar dryer with natural air convection for drying apricots.
Experience in the operation of the Heavy Residue Conversion Complex (HRCC) based on VCC technology
Authors: Shigabutdinov A K , Presnyakov V V , Idrisov M R , Novikov M A , Hramov A A , Urazaikin A S
Published: August 2022

The article presents a comparative assessment of various processes of demetallization of heavy petroleum feedstock (HPF). By the example of TAIF-NK JSC, which operates a slurry hydrocracking unit based on VCC process, the possibility of mastering secondary processes aimed at deepening oil refining is shown.
Geophysical surveys as a tool for geotechnical monitoring of disturbed land reclamation
Authors: Burlutsky S B
Published: August 2022

The article is devoted to the issues of controlling the reclamation of disturbed lands after the end of field development. It is proved that duration of transformation processes of the geological environment after a mine recultivation stage determines the necessity of control of the changes including the ones carried out by means of geophysical investigations. The way methods of engineering geophysics increase reliability of information about the state of stability of recultivated areas by the example of slope structures is shown. Proposals for the synthesis of geophysical and engineering-geological information in the framework of geotechnical monitoring of disturbed land reclamation are formulated with regard to the findings of the study.
Experimental study of heliothermal processing of municipal solid waste based on solar energy
Authors: Kodirov I N , Toshmamatov B M , Aliyarova L A , Shomuratova S M , Chorieva S
Published: August 2022

The article examines the sources of solid waste generation, their impact on the environment and human health. The morphological composition of municipal solid waste (MSW) and the factors influencing the dynamics of their change were analyzed. Based on the results of the study, the physical and thermal parameters of solid waste- ρ, φ were determined and the elemental composition and heat of combustion of solid waste were analyzed. It was found that the physical properties of MSW and the morphological composition of MSW depend on the seasons and other conditions. An energy balance diagram for heliothermal processing of solid household waste with different morphological compositions in a solar device for thermal treatment of solid waste was calculated and it was found that the share of solar energy for thermal processing of solid household waste was 78%. As a result of the thermal processing of organic compounds, which formed the morphological composition of the MSW, it was found that it is possible to obtain alternative fuels and produce thermal energy and electricity in the traditional way.
Environmental foundations of oil and gas production in the Russian Federation
Authors: Zhichkina L , Zhichkin K , Sharipov F F , Takhumova O V , Perfilyev A A , Temnyshov I A
Published: August 2022

The production of fossil fuels is associated with a significant burden on the environment. However, comparing the production of oil and gas with the extraction of other types of minerals, it can be seen that with significantly larger production volumes, the environmental impact is lower here. The purpose of the research is to study the impact of oil and gas production in Russia on the environment in comparison with the industry average situation. To do this, the following tasks are expected to be performed: - identifying the dynamics of the production of fuel resources in Russia in 2017-2020; - determination of indicators of environmental pollution and their comparison with industry averages; - calculation of current costs and investments in fixed assets for environmental protection. In this, first of all, a significant role is played by the features of the mining object, the technologies used and the need to maintain the status of an environmentally friendly industry due to the high share of exports. The main source of pollution is air emissions (hydrocarbons (including volatile organic compounds) - 44.6%, carbon monoxide - 36.3%, solids, sulfur dioxide, nitrogen oxides). Awareness of this problem is also manifested in the structure of investments in environmental protection. Their share in the protection of atmospheric air does not fall below 59% of the total amount of environmental investments.
On the issue of wastewater treatment with an organomineral sorbent obtained by electroplasmic processing of coal flotation tailings
Authors: Kondratenko A S , Buyantuev S L
Published: August 2022

The article considers the technology of obtaining organomineral sorbents with a highly developed porous structure from the waste of coal enrichment – carbon flotation tailings. The synthesis of sorbents was carried out using electric arc plasma with the development of a technique for obtaining combined sorbents used for wastewater treatment. The article presents data on the study of functional groups of coal-sludge raw materials to establish the composition and structure of the surface layer with the identification of the nature of surface compounds. The article also discusses a series of laboratory and industrial tests of the sorption-filtering properties of the obtained organomineral sorbents in wastewater treatment and water treatment.
Method for determining the optimal value of the specific heat capacity and temperature regime of a short-term heat accumulator of passive solar heating systems with a flat reflector of radiation
Authors: Dusyarov A S , Sh Ergashev U , Kholmanova O P
Published: August 2022

The article presents the results of the analysis and generalization of the experience of operating residential facilities with solar heating systems, even a slight accumulation of the daytime excess heat of solar radiation is determined, which can significantly increase the replacement coefficient of the heat load for heating the systems under consideration. An unjustified increase in the capacity of the heat accumulator has been determined that does not give a noticeable increase in the replacement coefficient for the heat load of the system. Studied and developed new and improved existing insolation passive solar heating systems. The article shows the results of the analysis and operation of residential buildings with solar systems, it is determined that a slight accumulation of daily excess heat of solar radiation can significantly increase the replacement coefficient for the heat load on the heating of the systems under consideration.
Digitalization of electrical systems and networks on the example of a digital substation
Authors: Krasovskaya O A , Xueyin C , Ibragimova A V , Bowen M , Nan Z
Published: August 2022

The article analyzes modern digital technologies in the energy industry on the example of digital substations. The basic principles and advantages of digital technologies are presented, and generally accepted principles are formulated. It is shown that event extraction and intelligent information processing are the necessary conditions for digitalization of the energy industry. Digital transformation is the introduction of modern technologies into the business processes of an enterprise, which implies fundamental changes in approaches to management, corporate culture, and external communications. Digitalization, Industry 4.0 and the Internet of Things can be called the components of digital transformation in the energy sector.
Modeling and calculation of the thermal balance of a pyrolysis plant for the production of alternative fuels from biomass
Authors: Mamatkulova S G , Uzakov G N
Published: August 2022

In this article, in order to determine the consumption of thermal energy for biomass processing, modeling and calculation of the thermal balance of a pyrolysis plant are performed. Based on these equations, the calculation of parameters such as the thermal balance for a tubular (cylindrical shape) bioreactor, the heat used, the efficiency of the tubular bioreactor, the exergy of the source fuel, the exergetic efficiency of the bioreactor, the loss of exergy to the environment, the heat transfer coefficient, etc. The heat balance calculation software is developed using the Java programming language. In addition, the article provides a comparative analysis of the technical and energy characteristics of bioenergy plants, which shows that the energy intensity of biomass processing in existing plants reaches up to 50-60% in the total heat balance
Improving the reliability of power supply facilities in the agro-industrial sector
Authors: Shatrov A F , Gaitova T B , Stushkina N A , Leshtayev O V , Sergeeva N A
Published: August 2022

This article presents a system for monitoring and diagnosing the performance of operating equipment, in particular power transformers. Since power transformers are the main element of an electrical installation, the reliability of the power supply system depends on their technical state (TS). In our country one of the promising systems for monitoring and diagnostics is Transformer Diagnostics Monitor. The authors have considered the algorithm of this monitoring system and the possibility of its application in digital substations (DSs). Implementation of Transformer Diagnostics Monitor in the automatic control system of a substation prevents electrical equipment from failing, reducing the economic damage from power shortage.
Determination of main energy parameters and efficiency of local energy system based on renewable energy sources
Authors: Urishev B , Kuvatov U , Umirov A
Published: August 2022

This article presents a methodology for determining the basic parameters of a local power system based on the use of wind, solar, hydropower devices and the hydraulic accumulation of some of their energy, including the maximum volume of the upper water basin. The results of calculations performed on the basis of this method determined the maximum volume of the water basin, which will allow to accumulate 14% of the energy produced in the local power system with a capacity of 18 MW. The cost-effectiveness and functional advantages of the method of hydraulic accumulation of energy adopted in this local power system over lithium-ion batteries have been identified.
Analysis of the impact of the energy industry on the environment
Authors: Zakharov S V , Lushpey V P , Abbasova L R , Zhongkai S
Published: August 2022

The article analyzes the issue of environmental pollution by the energy industry. Currently, the problems of environmental pollution are alarming, which is regularly discussed by the media and the scientific community. Over the past 20 years, many scientists have predicted death for the Earth if radical measures are not taken to save it. Due to the activities of enthusiasts and organizations, books and research papers have been written about pollution and its types; studies have been carried out on the consequences of environmental disasters in the world.
Environmental model using life cycle assessment and artificial intelligence techniques to predict impacts on industrial water treatment.
Authors: Jesus José de , Oliveira-Esquerre Karla , Medeiros Diego Lima
Published: August 2022

With the advancement of globalization, the growing demand for environmental resources in industrial processes and the increasing availability of data and information, the need to align data modeling concepts with Artificial Intelligence (AI) techniques and existing environmental tools has emerged. From a sustainability perspective, life cycle assessment (LCA) is an extremely important tool in ensuring adequate practices in environmental thinking. It is through the life cycle assessment (LCA) that it is possible to measure the environmental impacts from products and processes, as well as to make projections that minimize these impacts. This research employed an artificial intelligence (AI) methods, namely adaptive neurofuzzy inference system (ANFIS) model, to predict life cycle environmental impacts in industrial water treatment using aluminum sulfate and Tannin-Base biocoagulant. The results show that different AI algorithms are used to build LCA models. The AI algorithms in the studies work from problem identification to the solution stage, so the integration between AI and LCA makes it possible to build predictive machine learning models to enable assertiveness in decision making.
Mechanical Properties and Water Absorption of Glass Fiber Reinforced Composite Laminates made by Varying Stacking Sequence
Authors: Paglicawan Marissa A. , Emolaga Carlo S. , Custodio Cyron L. , Sudayon Johanna Marie B. , De Lara Ryan John L.
Published: August 2022

This study aims to demonstrate the effects of various stacking sequences of different glass fiber architecture forms on the mechanical properties of glass fibre reinforced polyester composites. The composites were manufactured by hand lay-up technique and its mechanical properties were characterized in terms of tensile, flexural, and drop-ball impact tests as well as water absorption. The mechanical properties of the glass fiber reinforced polyester were somewhat affected depending on the stacking sequences from single alternating order, double alternating order, and triple alternating order of chopped strand mat and plain-woven fabric piled in ten (10) to fourteen (14) layers. The laminates consisting of alternating sequence manner of plain-woven fabric and chopped strand mat stacked in different layers have no significant effect on the mechanical properties. Stacking sequence of double alternating layer piled in twelve (12) layers was found to have better tensile strength than single and double alternating order of two different glass fiber form while the triple alternating manner piled in twelve (12) layers resulted to higher tensile modulus. The double alternating order of different glass fiber forms stacked in twelve (12) layers resulted to an improvement in flexural properties. Some selected laminates exhibited no delamination in drop-ball impact test and minimal water absorption when immersed in water for 30 days for all the laminates.
Laser polarization driven micromanipulation and reorientation dynamics of an asymmetric shaped microscopic biomaterial using optical tweezers
Authors: D Chetana , P Praveen , B V Nagesh , Bhattacharya Sarbari , Ananthamurthy Sharath
Published: August 2022

We present measurements and a theoretical model that describes the dynamics of ellipsoidal shaped, chicken red blood cells (cRBCs) reorienting in an optical trap and demonstrates the ability to control their reorientation through changes in the intensity distribution that results from the different states of the polarization of the trapping laser. We have observed that in linearly polarized light, cRBC, a type of avian RBC, undergoes dual reorientation, with the first reorientation about the cell’s major axis and the second, about its short minor axis, with the major axis aligning with the laser propagation direction at equilibrium. We compute the work done for each of these reorientations and attribute the observed dynamics to a minimization of the energy cost for the particular sequence of the reorientations that we observe. Further, we achieve a controlled second orientation of the major axis along the laser propagation direction by varying the ellipticity of the polarization of the laser. We explain these partial second reorientation results by employing a geometrical optics-based model. Characterizing the dynamics and control of these regular-shaped natural soft materials through optical polarization is relevant in the context of current work in the design and development of microscopic artefacts such as lab-on-a-chip platforms.
Diffraction-free beam propagation at the exceptional point of non-Hermitian Glauber Fock lattices
Authors: Yuce Cem , Ramezani Hamidreza
Published: August 2022

We construct localized beams in a non-Hermitian Glauber Fock (NGF) lattice of coupled waveguides and show that they can propagate over a long distance withalmost no diffraction. We specifically obtain the diffraction-free beams in a finite NGF lattice at the exceptional point (EP) by using the exact eigenstates of the semi-infinite unidirectional NGF lattice. We provide a numerical approach to finding other lattices that are capable of supporting non-diffracting beams at EPs.
PhenoComb: a discovery tool to assess complex phenotypes in high-dimensional single-cell datasets
Authors: Burke Paulo E P , Strange Ann , Monk Emily , Thompson Brian , Amato Carol M , Woods David M
Published: August 2022

Motivation

High-dimensional cytometry assays can simultaneously measure dozens of markers, enabling the investigation of complex phenotypes. However, as manual gating relies on previous biological knowledge, few marker combinations are often assessed. This results in complex phenotypes with the potential for biological relevance being overlooked. Here, we present PhenoComb, an R package that allows agnostic exploration of phenotypes by assessing all combinations of markers. PhenoComb uses signal intensity thresholds to assign markers to discrete states (e.g. negative, low, high) and then counts the number of cells per sample from all possible marker combinations in a memory-safe manner. Time and disk space are the only constraints on the number of markers evaluated. PhenoComb also provides several approaches to perform statistical comparisons, evaluate the relevance of phenotypes and assess the independence of identified phenotypes. PhenoComb allows users to guide analysis by adjusting several function arguments, such as identifying parent populations of interest, filtering of low-frequency populations and defining a maximum complexity of phenotypes to evaluate. We have designed PhenoComb to be compatible with a local computer or server-based use.

Results

In testing of PhenoComb’s performance on synthetic datasets, computation on 16 markers was completed in the scale of minutes and up to 26 markers in hours. We applied PhenoComb to two publicly available datasets: an HIV flow cytometry dataset (12 markers and 421 samples) and the COVIDome CyTOF dataset (40 markers and 99 samples). In the HIV dataset, PhenoComb identified immune phenotypes associated with HIV seroconversion, including those highlighted in the original publication. In the COVID dataset, we identified several immune phenotypes with altered frequencies in infected individuals relative to healthy individuals. Collectively, PhenoComb represents a powerful discovery tool for agnostically assessing high-dimensional single-cell data.

Availability and implementation

The PhenoComb R package can be downloaded from https://github.com/SciOmicsLab/PhenoComb.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
CellSium: versatile cell simulator for microcolony ground truth generation
Authors: Sachs Christian Carsten , Ruzaeva Karina , Seiffarth Johannes , Wiechert Wolfgang , Berkels Benjamin , Nöh Katharina
Published: August 2022

To train deep learning-based segmentation models, large ground truth datasets are needed. To address this need in microfluidic live-cell imaging, we present CellSium, a flexibly configurable cell simulator built to synthesize realistic image sequences of bacterial microcolonies growing in monolayers. We illustrate that the simulated images are suitable for training neural networks. Synthetic time-lapse videos with and without fluorescence, using programmable cell growth models, and simulation-ready 3D colony geometries for computational fluid dynamics are also supported.

Availability and implementation

CellSium is free and open source software under the BSD license, implemented in Python, available at github.com/modsim/cellsium (DOI: 10.5281/zenodo.6193033), along with documentation, usage examples and Docker images.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Identification of bacteriophage genome sequences with representation learning
Authors: Bai Zeheng , Zhang Yao-zhong , Miyano Satoru , Yamaguchi Rui , Fujimoto Kosuke , Uematsu Satoshi , Imoto Seiya
Published: August 2022

Motivation

Bacteriophages/phages are the viruses that infect and replicate within bacteria and archaea, and rich in human body. To investigate the relationship between phages and microbial communities, the identification of phages from metagenome sequences is the first step. Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. Database-based methods typically use a large number of sequences as references; alignment-free methods usually learn the features of the sequences with machine learning and deep learning models.

Results

We propose INHERIT which uses a deep representation learning model to integrate both database-based and alignment-free methods, combining the strengths of both. Pre-training is used as an alternative way of acquiring knowledge representations from existing databases, while the BERT-style deep learning framework retains the advantage of alignment-free methods. We compare INHERIT with four existing methods on a third-party benchmark dataset. Our experiments show that INHERIT achieves a better performance with the F1-score of 0.9932. In addition, we find that pre-training two species separately helps the non-alignment deep learning model make more accurate predictions.

Availability and implementation

The codes of INHERIT are now available in: https://github.com/Celestial-Bai/INHERIT.

Supplementary information

Supplementary data are available at Bioinformatics online.
Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet
Authors: Hardisty Alex R , Ellwood Elizabeth R , Nelson Gil , Zimkus Breda , Buschbom Jutta , Addink Wouter , Rabeler Richard K , Bates John , Bentley Andrew , Fortes José A B , Hansen Sara , Macklin James A , Mast Austin R , Miller Joseph T , Monfils Anna K , Paul Deborah L , Wallis Elycia , Webster Michael
Published: August 2022

The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.
Culture and Quality Matter in Building Effective Mentorship Relationships with Native STEM Scholars
Authors: Estrada Mica , Young Gerald , Flores Lilibeth , Hernandez Paul R , Hosoda K Kanoho , DeerInWater Kathy
Published: August 2022

Native peoples (Native American, Alaskan Native, Native Hawaiian) are underrepresented in academia; they represent 2% of the US population but 0.01% of enrolled undergraduate students. Native peoples share the experiences of colonization and forced assimilation, resulting in the loss of ancestral knowledge, language, and cultural identity. Recognizing history and the literature on social integration and mentorship, we followed 100 Native science and engineering scholars across a year of participation in the hybrid American Indian Science and Engineering Society mentorship program. The results showed that high-quality faculty mentorship predicted persistence a year later. Furthermore, mentors who shared knowledge of Native culture—through experience or shared heritage—uniquely contributed to the Native scholars’ social integration and persistence through scientific community values in particular. Therefore, Native scholars may benefit from mentorship supporting the integration of their Native culture and discipline rather than assimilation into the dominant disciplinary culture.
Coronavirus Disease 19 (COVID-19) Vaccine Effectiveness Against Symptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Delta-Dominant and Omicron-Dominant Periods in Japan: A Multicenter Prospective Case-control Study (Factors Associated with SARS-CoV-2 Infection and the Effectiveness of COVID-19 Vaccines Study)
Authors: Arashiro Takeshi , Arima Yuzo , Muraoka Hirokazu , Sato Akihiro , Oba Kunihiro , Uehara Yuki , Arioka Hiroko , Yanai Hideki , Kuramochi Jin , Ihara Genei , Chubachi Kumi , Yanagisawa Naoki , Nagura Yoshito , Kato Yasuyuki , Ueda Akihiro , Numata Akira , Kato Hideaki , Ishii Koji , Ooki Takao , Oka Hideaki , Nishida Yusuke , Stucky Ashley , Smith Chris , Hibberd Martin , Ariyoshi Koya , Suzuki Motoi
Published: August 2022

Background

Although several coronavirus disease 2019 (COVID-19) vaccines initially showed high efficacy, there have been concerns because of waning immunity and the emergence of variants with immune escape capacity.

Methods

A test-negative design case-control study was conducted in 16 healthcare facilities in Japan during the Delta-dominant period (August-September 2021) and the Omicron-dominant period (January-March 2022). Vaccine effectiveness (VE) against symptomatic severe acute respiratory syndrome coronavirus 2 infection was calculated for 2 doses for the Delta-dominant period and 2 or 3 doses for the Omicron-dominant period compared with unvaccinated individuals.

Results

The analysis included 5795 individuals with 2595 (44.8%) cases. Among vaccinees, 2242 (55.8%) received BNT162b2 and 1624 (40.4%) received messenger RNA (mRNA)-1273 at manufacturer-recommended intervals. During the Delta-dominant period, VE was 88% (95% confidence interval [CI], 82–93) 14 days to 3 months after dose 2 and 87% (95% CI, 38–97) 3 to 6 months after dose 2. During the Omicron-dominant period, VE was 56% (95% CI, 37–70) 14 days to 3 months since dose 2, 52% (95% CI, 40–62) 3 to 6 months after dose 2, 49% (95% CI, 34–61) 6+ months after dose 2, and 74% (95% CI, 62–83) 14+ days after dose 3. Restricting to individuals at high risk of severe COVID-19 and additional adjustment for preventive measures (ie, mask wearing/high-risk behaviors) yielded similar estimates, respectively.

Conclusions

In Japan, where most are infection-naïve, and strict prevention measures are maintained regardless of vaccination status, 2-dose mRNA vaccines provided high protection against symptomatic infection during the Delta-dominant period and moderate protection during the Omicron-dominant period. Among individuals who received an mRNA booster dose, VE recovered to a high level.
Coenzyme Q10 Levels Associated With Cognitive Functioning and Executive Function in Older Adults
Authors: Fernández-Portero Cristina , Amián Josué G , Bella Rocío de la , López-Lluch Guillermo , Alarcón David
Published: July 2022

Brain deterioration with age is associated with inflammation and oxidative stress that result in structural and functional changes. Recent studies have indicated that coenzyme Q10 (CoQ10) is associated with neurological oxidative stress and cognitive impairment. Studies with older people have shown a relationship between neurodegenerative diseases and CoQ10 levels. However, no studies have analyzed the relationship between CoQ10 and cognitive functioning in older adults. The aim of this study was to analyze the association between CoQ10 and cognitive functioning in an older adult sample, controlling for other factors that may influence aging, such as the level of physical activity and nutritional status. The sample consisted of 64 older adults aged 65–99 years (76.67 ± 8.16 years), among whom 48 were women (75%). The participants were recruited among those who attended community centers to voluntarily participate in leisure activities. According to previous studies, physical activity and nutritional status are positively associated with cognitive functioning. However, the main finding of this study was that plasma CoQ10, controlling for other measures, was significantly associated with cognitive functioning and executive function. The current findings suggest that a decline in cognitive capacities may be related to reduced antioxidant defenses, as reflected by low CoQ10 levels in older adults.
Perceptions on Oral Care Needs, Barriers, and Practices Among Managers and Staff in Long-Term Care Settings for Older People in Flanders, Belgium: A Cross-sectional Survey
Authors: Palmers Ellen , Janssens Lynn , Phlypo Inès , Vanhaecht Kris , De Almeida Mello Johanna , De Visschere Luc , Declerck Dominique , Duyck Joke
Published: August 2022

Background and Objectives

This study aimed to explore oral health perception and oral care needs, barriers, and current practices as perceived by managers and staff in long-term care organizations for older people in Flanders.

Research Design and Methods

This is a cross-sectional study where 2 questionnaires were developed, one for managers and one for caregivers, and were validated in Flemish long-term care organizations. Descriptive analyses and multivariable generalized linear models evaluated the main outcomes and their associations with determinants such as the size of the organization, the presence of an oral health policy, collaboration with a dentist, among others.

Results

A total of 145 managers and 197 caregivers completed the questionnaire. More than 50% of caregivers and managers perceived their residents’ oral health as mediocre to good. Collaboration with a dentist (B = 0.84) and oral health care involvement (B = 0.08) within the organization showed a strong association with a positive perception of oral health. Lack of time (57%) and care resistance (70%) were the most important barriers perceived by caregivers. Guidelines concerning oral care were not available or were unknown to 52% of the caregivers. Having an oral health policy within the organization was strongly associated with the correct use of guidelines for daily care of natural teeth (B = 1.25) and of dental prosthesis (B = 1.15).

Discussion and Implications

The results emphasize that collaborating with a dentist and the presence of an oral health policy in care organizations are important for a positive perception of the oral health of the residents and for the adoption of guidelines by caregivers and managers. In addition, training on handling care refusal should be included in the overall training. These results are crucial input for the development of a methodology for implementing a structured oral care policy in long-term care facilities.
What are the tuberculosis care practices of informal healthcare providers? A cross-sectional study from Eastern India
Authors: Thapa Poshan , Hall John J , Jayasuriya Rohan , Mukherjee Partha Sarathi , Beek Kristen , Das Dipesh Kr , Mandal Tushar , Narasimhan Padmanesan
Published: August 2022

India is the highest TB burden country, accounting for an estimated 26% of the global TB cases. Systematic engagement of the private sector is a cornerstone of India’s National Strategic Plan for TB Elimination (2017–25). However, informal healthcare providers (IPs), who are the first point of contact for a large number of TB patients, remain significantly underutilized in the National TB Elimination Program of India. Non-prioritization of IPs has also resulted in a limited understanding of their TB care practices in the community. We, therefore, undertook a descriptive study to document IPs’ TB care practices, primarily focusing on their approach to screening, diagnosis, treatment and referral. This cross-sectional study was carried out from February to March 2020 in the Birbhum District of West Bengal, India. Interviews were conducted utilizing the retrospective case study method. A total of 203 IPs participated who reported seeing at least one confirmed TB patient in 6 months prior to the study. In that duration, IPs reported interacting with an average of five suspected TB cases, two of which were later confirmed as having TB. Antibiotic use was found to be common among IPs (highest 69% during the first visit); however, they were prescribed before the patient was suspected or confirmed as having TB. We noted the practice of prolonged treatment among IPs as patients were prescribed medicines until the second follow-up visit. Referral was the preferred TB case management approach among IPs, but delayed referral was observed, with only one-third (34%) of patients being referred to higher health facilities during their first visit. This study presents important findings on IPs’ TB care practices, which have consequences for achieving India’s national goal of TB elimination.
How to do (or not to do)…using causal loop diagrams for health system research in low and middle-income settings
Authors: Cassidy Rachel , Borghi Josephine , Semwanga Agnes Rwashana , Binyaruka Peter , Singh Neha S , Blanchet Karl
Published: August 2022

Causal loop diagrams (CLDs) are a systems thinking method that can be used to visualize and unpack complex health system behaviour. They can be employed prospectively or retrospectively to identify the mechanisms and consequences of policies or interventions designed to strengthen health systems and inform discussion with policymakers and stakeholders on actions that may alleviate sub-optimal outcomes. Whilst the use of CLDs in health systems research has generally increased, there is still limited use in low- and middle-income settings. In addition to their suitability for evaluating complex systems, CLDs can be developed where opportunities for primary data collection may be limited (such as in humanitarian or conflict settings) and instead be formulated using secondary data, published or grey literature, health surveys/reports and policy documents. The purpose of this paper is to provide a step-by-step guide for designing a health system research study that uses CLDs as their chosen research method, with particular attention to issues of relevance to research in low- and middle-income countries (LMICs). The guidance draws on examples from the LMIC literature and authors’ own experience of using CLDs in this research area. This paper guides researchers in addressing the following four questions in the study design process; (1) What is the scope of this research? (2) What data do I need to collect or source? (3) What is my chosen method for CLD development? (4) How will I validate the CLD? In providing supporting information to readers on avenues for addressing these key design questions, authors hope to promote CLDs for wider use by health system researchers working in LMICs.
Huntingtin turnover: modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550
Authors: Lee Yejin , Kim Hyeongju , Barker Douglas , Vijayvargia Ravi , Atwal Ranjit Singh , Specht Harrison , Keshishian Hasmik , Carr Steven A , Lee Ramee , Kwak Seung , Hyun Kyung-gi , Loupe Jacob , MacDonald Marcy E , Song Ji-Joon , Seong Ihn Sik
Published: July 2022

Huntington’s disease (HD) is a neurodegenerative disorder caused by an inherited unstable HTT CAG repeat that expands further, thereby eliciting a disease process that may be initiated by polyglutamine-expanded huntingtin or a short polyglutamine-product. Phosphorylation of selected candidate residues is reported to mediate polyglutamine-fragment degradation and toxicity. Here to support the discovery of phosphosites involved in the life-cycle of (full-length) huntingtin, we employed mass spectrometry-based phosphoproteomics to systematically identify sites in purified huntingtin and in the endogenous protein by proteomic and phosphoproteomic analyses of members of an HD neuronal progenitor cell panel. Our results bring total huntingtin phosphosites to 95, with more located in the N-HEAT domain relative to numbers in the Bridge and C-HEAT domains. Moreover, phosphorylation of C-HEAT Ser2550 by cAMP-dependent protein kinase (PKA), the top hit in kinase activity screens, was found to hasten huntingtin degradation, such that levels of the catalytic subunit (PRKACA) were inversely related to huntingtin levels. Taken together, these findings highlight categories of phosphosites that merit further study and provide a phosphosite kinase pair (pSer2550-PKA) with which to investigate the biological processes that regulate huntingtin degradation and thereby influence the steady state levels of huntingtin in HD cells.