bluuebunny/crossref_metadata_2025 huggingface dataset:
Locating Site Selection for Rainwater Harvesting Structure using Remote Sensing and GIS
Authors: Khudhair M A , Sayl K N , Darama Y
Published: August 2020

Rainfall is a key source to diminish the problem of water scarcity in the arid and semi-arid regions. Rainwater harvesting is considered an imperious tool for rainwater conservation. Locating the appropriate location for rainwater harvesting structure plays an important role to increase water availability and improve water resources planning. The main goal of this paper is to recognize the proper location for a rainwater harvesting structure using a suitability model generated with ModelBuilder in ArcGIS. Six thematic layers i.e. soil structure, slope, drainage density, vegetation cover, distance to the roads, and runoff depth, are considered to find the proper site for rainwater harvesting structure. The result shows that 12% represents the suitable zone of the total study area, 42% represents the medium suitable area, and 46% represents not suitable areas to implement rainwater harvesting structure. The application of this scheme should maintain any policy adoption for site selection for rainwater harvesting.
Mechanical and sustainability assessment of induction heatable asphalt tiles and asphalt pellets in road maintenance
Authors: Obaidi Hadel
Published: August 2020

In this paper, two new methods for pothole repairing are proposed, assessed and compared. The first method is a combination of a prefabricated asphalt tile and a bonding layer that can be placed into a sanitized pothole and bonded by applying electromagnetic induction heating. The second approach consists of the prefabrication of asphalt pellets that can directly fill a given pothole and be heated by induction. By combining prefabrication and on-site induction heating, both methods offer high-quality mechanical performance while reducing the production of debris and noxious fumes. They can also improve work conditions for operators and the cost/time efficiency of road maintenance. In this research, both technologies were experimentally assessed through mechanical properties, such as tensile and shear strength and demonstrated by repairing potholes previously created on testing slabs and subjected to wheel tracking tests. Furthermore, the innovative patching materials have been evaluated from energy consumption. Both methods obtained very satisfactory results, showing excellent durability much more similar to a new road than to a road repaired with current techniques frequently used.
Change in land-uses of Ramadi city and its influence on public transportation sustainability
Authors: Ahmed N. A. , Mahmood T. S.
Published: August 2020

The transportation system in the city of Ramadi, like other Iraqi cities, suffers from many problems for many reasons, notably, changing land uses there. Since the mid-nineties, the change from residential to commercial use was common in Ramadi, and the absence of successful and sustainable planning has exacerbated the problems more due to a large number of planning violations. Here lies the problem of the study, which is the negative impact of the change on the sustainability of urban transportation. In order to address such problems, there is a need for in-depth knowledge of the impact ratios and their reasons for resolving the various transportation changes under study, which is the sustainability of public transport for its significance, and it is deeply affected by changes in land uses. The aim of the study stems from impact standardization and its spatial location and analyzing it by using geographic information systems. The model can be adopted and circulated to the rest of the Iraqi cities in order to present a vision to address the negative impact resulting from the change in land uses and to achieve the goals of sustainable planning for the urban area.
Municipal Waste Water Treatment Using Sequencing Batch Reactor (SBR)
Authors: Mohammed H.M , Kheria M.E
Published: August 2020

The sequencing batch reactor (SBR) method was used throughout this research; the experiments were carried out at the site of the Zafaraniya (MBR) project. This system has also the advantages of low initial and performance costs. Different time periods were used in this study ranging (3-8) hours for 9 months, the tests has been conducted in the environmental laboratory of the Zafaraniya (MBR) project. The removal efficiency of PO4 from waste water depends on the change of anoxic conditions to aerobic. This efficiency is a maximum when the periods of the two types of conditions are equal; the removal of NO3 depends on food supply for micro-organisms which convert nitrates to nitrogen gas under anoxic conditions so it is change able. According to the results gained, this kind of treatment could be used to removal phosphates & nitrates from waste waters, several experiments were conducted for the process and with different times that occur in a reactor (SBR) to reach the appropriate time to remove all pollutants from the waste water. The removal ratio was achieved when the time of the anaerobic process was equal to the time of the aerobic process that followed it. High removing efficiency in the pollutants was obtained. Phosphorous and nitrate from waste water, the percentages of removal were reached at (91.3% & 98%) for PO4 and NH3 relatively.
Removal of Heavy Metals from Wastewater Using Pomegranate Peel
Authors: Rashed Musaab K. , Tayh Wissam
Published: August 2020

Research was undertaking to evaluate the ability of pomegranate peel in removing heavy metal cations Cu+2, Cd+2 & Zn+2 from wastewater. Simulated artificial water via batch adsorption approach was used in this study. Pomegranate peel was cleaned thoroughly to remove dust and dirt before drying them. Next, the peels were grinded (approximately less than 1mm in size) and directly used in different adsorbent/metal ion ratios. The metal ion concentration begins from 1000 ppm. The effect of contact duration, initial concentration of metal ion and loading weight of adsorbent on the percentage of heavy metal removal were investigated. The experiment was conducted at room temperature of 25 °C and pH value was maintained at the range of 5 to 6. From the observation and analysis, it was found that pomegranate peel successfully removed the heavy metals. The removal percentage observed was 80% for Cu+2 ions, 50.5% for Cd+2 ions and 32.5% for Zn+2 ions. The removal percentage was achieved within an hour of contact with an adsorbent loading ratio of 30 g/l. However, the removal percentage of mixed ions was relatively low, resulting from competition and interaction between the ions. The Pomegranate peel is available in huge quantities, low cost and can be used as an efficient metal ion adsorbent.
Performance of Oil on Bio-Methane Creation under Anaerobic Co-Fermentation Condition. Review
Authors: Alhraishawi A A. , Alani W K , Chaichan M T , Jawad R S
Published: August 2020

Anaerobic fermentation of oil is becoming appealing benefit due to its high biodegradation in outputting biogas. Due to a complex synthesis organic wastes, oil has been inspected as potency the substrate to output biogas when fermented under non-aerobically as compared to {carbohydrate and protein}. However, it is familiar that oil degradation leads to inhibition of biogas creation with delay phase occurrence, sewage floatation, and failure. Co-fermentation of oil wastes has offered a promotion to bio methane creation of reducing decomposition of the bacteria but the test of slow ‘hydrolysis’ due to inhibition still takes place. Long-chain fatty acids (LCFAs) generated during hydrolysis is recognized as firstly inhibitor due to its poisoning influences on cell wall adsorption by communities bacteria. This research reviews the scientific previously literature on biogas creation, ways to minimize oil discouraged in promotion biogas creation.
The x-ray diffraction study of the composition of the powder materials from the waste steel X13
Authors: Ageeva E.V. , Khardikov S.V. , Novikov A. N.
Published: August 2020

To restore and protect the surfaces of parts using a layer of molten metal, various methods of surfacing are used, differing from each other by melting methods and compositions of the welding medium: electric arc, flame, plasma, laser, induction, etc. With this technology, metals of various chemical composition, including copper, bronze, cast iron, as well as nickel, cobalt and chromium alloys can be deposited on the working surfaces of steel structures. There are several ways to obtain such powder materials. The most promising method for obtaining powder materials is the electro-erosion dispersion method (EED), which is distinguished by its ecological purity of the process and relatively low energy expenditure. To study the structure of the particles of the obtained powders, their X-ray structural analysis was performed on a RigakuUltima IV X-ray diffractometer.
X-ray diffraction analysis of sintered products from electro-erosion materials, obtained from Cr17 alloy waste
Authors: Sysoev A A , Grashkov SA , Pivovar NA
Published: August 2020

This article presents the phase composition study of sintered samples from electro-erosion materials of the Cr17 alloy, obtained in lighting kerosene. It was established that the main phases in the sintered sample are FeCr0,29Ni0,16C0,06, Cr, Cr7C3.
Texture and anisotropy of the mechanical properties of 2 mm sheets of Mg-9Li-3Al-0.4Ce alloy
Authors: Ya Betsofen S , Grushin I A , Petrov A A , Speransky K A
Published: August 2020

The phase composition, texture and anisotropy of the mechanical properties of 2 mm sheets of Mg-9Li-3Al-0.4Ce alloy were studied by X-ray diffraction and mechanical tests. It is shown that the alloy contains two solid solutions, the α phase with HCP lattice based on Mg and the β phase with BCC lattice based on Li. Intermetallic Al12Mg17 is also present in the alloy. Alloy sheets are characterized by a basal α-phase texture. At the same time, the most durable prismatic orientations are mainly located in the transverse rolling direction (TD), which leads to higher strength properties in this direction compared to the rolling direction (RD). The texture of the basicβ-phase in RD and TD does not differ and, accordingly, does not contribute to the anisotropy of strength properties.
Improving the reliability of metal structures of buildings and structures during reconstruction
Authors: Mezentseva A , Gel’manova Z , Konakbayeva A
Published: August 2020

Recently, the direction of prestressing metal structures, the regulation of forces in which is made by various methods without the use of high-strength steel is one of the hot spots of research. In this paper, an unconventional method for creating pre -stress in tubular elements using an expanding substance is applied. As used by a non-explosive destructive mixture (NDM).
Increasing the operational reliability of car variators due to creating regular surface microrelief by laser ablation
Authors: Yagyaev Elmar , Shron Leonid , Meniuk Dmitriy
Published: August 2020

The paper analyzes the car variator reliability issue. The variator performance is ensured by the surface layer quality, manufacturing accuracy, and the pulley and steel V-belt surface microrelief. The decisive factor in ensuring the variator reliability is the pulley finishing technique. Creating regular microreliefs on the finished pulley surface by laser ablation has been proposed, which act as micro-channels to improve the drainage of oil from the contact pattern. Creating oil channels on the pulley surface by laser ablation will ensure their arrangement and allow obtaining the desired pattern, direction, depth, and length.
Development and experimental studies of new types of sheet metal stamping equipment
Authors: Yu Botashev A , Bayramukov R A , Bisilov N U , Malsugenov R S
Published: August 2020

In this paper, developed devices for gas sheet stamping are presented. The devices allow to significantly reduce the cost of products. They can be used both for food manufacturing, petrochemical industry and other branches of industry. Prototypes of products obtained experimentally are presented.
Theoretical calculations of mechanotermic destruction process with regard to general rubber goods
Authors: Ametov I E , Abkhairova C V
Published: August 2020

Reference data on the properties of rubbers and some fillers included in their composition are considered. Based on them, the values of electric and thermal power necessary for the processing of waste tires and other rubber products are calculated. The calculations showed the undoubted advantage of the mechanothermal destruction of rubber products in comparison with the classical pyrolysis methods.
Biopolymer bindings for casting manufacturing processes on the technological lignin basis
Authors: Svinoroev Yu A , Dyadichev V V , Ternovskoy O A , Dyadicheva I V , Yu Melnik A , Ye Chornobay S
Published: August 2020

The paper analyzes the problem of using technological lignins to make new bindings for casting manufacturing processes. The reasons, restraining their application in casting manufacture, are considered. The objective (based on the physical nature of the material) and subjective (based on commercial benefit) reasons are presented. The paper considers the perspectives of application of technological lignins by the example of technological lignosulfonates use which is the main representative of the technological lignins family on the Russian market of bindings.
The study of contact electrical resistance of coatings on the basis of refractory metal alloys Co-W, Co-Mo, Ni-W, Ni-Mo
Authors: Gololobov G P , Suvorov D V , Serpova M A , Arefiev A S
Published: August 2020

The paper presents the research into contact electrical resistance of coatings on the basis of refractory metal alloys Co-W, Co-Mo, Ni-W, Ni-Mo. SEM-images of the tested samples’ surface are presented, and the peculiarities of their microrelief are analyzed. The results of the research are presented as dependencies of contact electrical resistance on the sample electrode pressing force for each type of the surface. The comparative analysis of them is done.
Quantitative phase analysis of Mg-Al-Zn and Mg-Zn-Zr alloys
Authors: Chernysheva Yu V , Grushin I A , Voskresenskaya I I , Savostin D S
Published: August 2020

Absract. A quantitative method has been developed for the phase analysis of magnesium alloys of the Mg-Zn-Al (MA2-1 and MA5) and Mg-Zn-Zr (MA14) systems based on the measurement of the lattice parameters of a solid solution, the use of Vegard’s law, and balance equations of chemical and phase composition. Examples of the application of the technique for assessing changes in the content of alloying elements in a solid solution and the number of intermetallic phases as a result of heat treatment of MA2-1 alloy are presented.
Effect of bias voltage on the texture of the TiN and ZrN coatings deposited by vacuum ion-plasma method
Authors: Ashmarin A A , Ya Betsofen S , Petrov L M , Lebedev M A
Published: August 2020

An X-ray diffraction method was used to study the formation of the crystallographic texture of vacuum ion-plasma TiN and ZrN coatings depend on the bias voltage on the substrate. It is shown that, at high values of the bias voltage (-100 V), a pronounced texture forms in TiN coatings and a two-component (111) + (113) texture in ZrN coatings. A decrease of the bias voltage to –10 V leads to a twofold increase in the hardness of the coatings, a non-texture state of TiN, and a weakening of the texture of ZrN coatings.
Effects of «simplest» post-treatment techniques on the composition of porous silicon surface
Authors: Lenshin A S , Chernousova O V , Seredin P V , Barkov K A , Minakov D A
Published: August 2020

The article is concerned with the investigation of techniques of post-treatment of porous silicon. It was shown that the applied techniques have considerable effect on por-Si nanowires shell without a considerable influencing on their core. To study the features of changing the phase composition and the composition of chemical bonds of the surface of porous silicon, we used infrared spectroscopy, Ultrasoft X-Ray Spectroscopy and photoluminescence spectroscopy.
Technologies of reusing materials obtained during step-by-step demolition of buildings
Authors: Zolotukhin S N , Volokitin V P , Kovalev N M
Published: August 2020

Nowadays scientists are required to create closed-cycle technologies for handling the waste; they have to reduce the waste amounts and the anthropogenic carbonic trace on the Earth, and they are supposed to use the recycled materials. The main amounts of the construction waste at the landfills of solid domestic waste appear after using the explosion method and the mechanical way of destruction, which are used for the demolition of buildings. Smart demolition, used during the renovation in Moscow, assumes crushing the obtained stone materials for their reuse. However, technologically crushing is not always possible, and economically it is cost-based. The research of the durability characteristics of load-bearing elements of the demolished buildings and existing regulatory documents allow reusing of these materials.
Calculation update of strength of expanded clay fiber-reinforced concrete elements with mixed reinforcement
Authors: Mailyan D R , Blyagoz A M , Kretinin K M
Published: August 2020

The paper deals with the methodology for calculating the strength of the expanded clay fiber-reinforced concrete elements with mixed reinforcement with the most complete view of the post-yield properties of prestressed and non-stressed rebars, as well as the influence of prestressing on the properties of the expanded clay fiber-reinforced concrete.
Investigation on bond performance between different types of FRP -reinforcedrebars and concrete
Authors: Komarov A I , Makarova N V , Tsuprik V G
Published: August 2020

In this paper the test results of a study on the bond behaviour of FRP bars to finegrained concrete are presented. Five series of concrete cylinders reinforced with basalt-reinforced polymer (BFRP) and glass fiber-reinforced polymer (GFRP) bars are tested in direct pullout conditions. As well as two series with steel bars are tested for comparison. For each specimen, the bond failure mode, the average bond strength, the initial bond stiffness, and the load–strain relationship curves and bar relative extension were analysed. Test results demonstrate the promise of using the FRP bars as an alternative to the steel bars in reinforcing concrete elements.
Coordinating metal Co2+ and Zn2+ compounds with acetylsalicylic acid: the influence on the cardiorespiratory system
Authors: Yu Ravaeva M , Chuyan E N , Cheretaev I V
Published: August 2020

The paper researches the effect of cobalt (ACCo2+) and zinc (ACZn2+) acetylsalicylates in doses of 5 and 10 mg/kg on the characteristics of the rats’ cardiorespiratory system. It is ascertained that coordinating metal compounds with the acetylsalicylic acid have a more pronounced biological effect in comparison with a monocompound of the acetylsalicylic acid; this makes the further search for coordinating compounds’ effects more prospective.
Improvement of high-speed steel cutting tool production technology using the method of nanostructure generation by laser ablation
Authors: Yagyaev Elmar , Akimov Seran
Published: August 2020

The article reveals a problem of improving the production technology of cutting tools made of high-speed steels by the method of generating nanostructures on their surface with the help of laser ablation. The spiked microstructures obtained on the surface of the instrument are coated with nanostructures. Experimental studies to modify the surfaces of cutting tools with laser ablation method are performed in air and in liquids. As a result of the analysis of the experimental samples surface morphology we can conclude that the modification of the surface of cutting tools made of P6M5 high-speed steel with laser pulses of nanosecond duration can be used in air and in liquids as a method of increasing the resistance characteristics of a cutting tool.
Temperature dependence of Ge2Sb2Te5 conductivity and its change during aging
Authors: Vorobyov Y V , Yakubov A O , Ermachikhin A V
Published: August 2020

Results of studies of conductivity activation energy and its evolution during the aging process are presented for the common phase change material Ge2Sb2Te5. The evolution of temperature dependence of conductivity during quasi-isothermal annealing are interpreted in the framework of simple Arrhenius model as the change of two corresponding parameters: activation energy and pre-exponential factor. It is shown, that the change in resistivity of the Ge2Sb2Te5 during aging is attributed to the simultaneous change of both parameters of the Arrhenius equation, that is, activation energy and pre-exponential factor. Temperature dependencies of those parameters are shown as well, and the Meyer-Neldel rule for conductivity of Ge2Sb2Te5 is tested on the basis of the obtained data.
Experimental evaluation of the efficiency of lubricating process media during the running-in period of a metal-cutting tool
Authors: Skakun Vladimir , Dzhemalyadinov Ruslan , Abdulkerimov Ilimdar
Published: August 2020

The possibility of increasing the durability of a cutting insert made of high-speed steel with a wear-resistant TiN coating due to the use of lubricating process media during the running-in period of the cutting tool is considered. Based on the analysis of the data obtained, an analogy in the mechanisms of the hardening action of the refrigerant and wear-resistant coatings is presented. It is shown that the durability of a metal-cutting tool substantially depends on the initial conditions of its operation.
Electron population properties with different energies in a helicon plasma source
Authors: ZHANG Zun , ZHANG Zhe , TANG Haibin , OUYANG Jiting
Published: August 2020

The characteristics of electrons play a dominant role in determining the ionization and acceleration processes of plasmas. Compared with electrostatic diagnostics, the optical method is independent of the radio frequency (RF) noise, magnetic field, and electric field. In this paper, an optical emission spectroscope was used to determine the plasma emission spectra, electron excitation energy population distributions (EEEPDs), growth rates of low-energy and high-energy electrons, and their intensity jumps with input powers. The 56 emission lines with the highest signal-to-noise ratio and their corresponding electron excitation energy were used for the translation of the spectrum into EEEPD. One discrete EEEPD has two clear different regions, namely the low-energy electron excitation region (neutral lines with threshold energy of 13–15 eV) and the high-energy electron excitation region (ionic lines with threshold energy ≥19 eV). The EEEPD variations with different diameters of discharge tubes (20 mm, 40 mm, and 60 mm) and different input RF powers (200–1800 W) were investigated. By normalized intensity comparison of the ionic and neutral lines, the growth rate of the ionic population was higher than the neutral one, especially when the tube diameter was less than 40 mm and the input power was higher than 1000 W. Moreover, we found that the intensities of low-energy electrons and high-energy electrons jump at different input powers from inductively coupled (H) mode to helicon (W) mode; therefore, the determination of W mode needs to be carefully considered.
Follow-up of a Wuqinxi exercise at home programme to reduce pain and improve function for knee osteoarthritis in older people: a randomised controlled trial
Authors: Xiao Chun Mei , LI Jing Jing , Kang Yong , Zhuang Yong Chang
Published: August 2020

Background

Exercise therapy is a key intervention in the management of knee osteoarthritis (KOA) and recommended in international guidelines on KOA management. An effective home-exercise programme for frail older adults with KOA was successful in achieving high adherence. This randomised controlled trial was to compare the adherence to the exercise and lasting effects of follow-up 3 months.

Methods

Sixty-eight participants in the original Wuqinxi (WQX) exercise study were community dwelling older adults (age = 70.95 ± 9.85 years) with KOA were categorised into 34 controls group, 34 WQX group adherers. The Western Ontario and Mc Master Universities Osteoarthritis Index questionnaire score (WOMAC) pain and Berg Balance Scale, Timed Up and Go Test, 6-min Walk Test, 30-s chair stand test, isokinetic muscle strength testing of knee flexion and extension measured at pre-test and post-test of the intervention period and follow-up for two groups.

Results

The WQX group maintained or improved in all nine measures from post-test to follow-up, whereas the control group significantly declined in WOMAC pain, Knee extensor strength and Knee flexor strength.

Conclusion

The WQX programme was an effective home-exercise programme that achieves high adherence in older adults with KOA who lived in these communities.
Transcriptome analysis in osmo-primed tomato seeds with enhanced longevity by heat shock treatment
Authors: Barbosa Batista Thiago , Javier Fernandez Geysson , Alexandre da Silva Tiago , Maia Júlio , Amaral da Silva Edvaldo Aparecido
Published: August 2020

Seed priming is widely used in commercial seeds and its main function is to accelerate and synchronize seed germination. Undesirably, primed seeds show reduced longevity and treatments like heat shock have been shown to improve longevity in primed seeds. Nonetheless, the effect of heat shock treatment on primed seeds at the mRNA level is not known. Thus, the aim of this work was to investigate the effect of heat shock treatment on the longevity of primed tomato (Solanum lycopersicum) seeds at the physiological and transcriptome levels. Tomato seeds were primed and dried (control). Alternatively, primed seeds were subjected to heat shock treatment (38 °C/32 % relative humidity) before drying. Germination, vigor and longevity were evaluated. Transcriptome analysis was performed by RNA sequencing (RNA-seq) from biological samples collected immediately after priming and another samples collected from primed seeds followed by the heat shock treatments. The gene expression was validated by quantitative real time PCR (RT-qPCR). We showed that applying heat shock treatment after priming increased germination speed, enhanced seed longevity and preserved the vigor during storage of primed tomato seeds. Through transcriptome analysis, 368 differentially expressed genes were identified, from which 298 genes were up-regulated and 70 were down-regulated. We showed the increase of mRNA levels of HEAT SHOCK FACTOR-like and HEAT SHOCK PROTEIN-like chaperone genes, suggesting the involvement of the proteins coded by these transcripts in the enhancement of longevity in primed tomato seeds. The heat shock treatment after priming enhances and preserves the vigor of tomato primed seeds during storage. In addition, improves seed longevity through the increase in the expression of transcripts related to protection by response to stress.
Fine Wrinkle Treatment and Hydration on the Facial Dermis Using HydroToxin Mixture of MicroBotox and MicroHyaluronic Acid
Authors: Kim Jong Seo
Published: August 2020

Background

Hyaluronic acid (HA) is a key contributor to skin moisture (hydration), and MicroBotox demonstrates improvements for fine wrinkles of the face.

Objectives

The author sought to evaluate the safety and efficacy of intradermal injection of hydrotoxin (combined mixture of MicroHA and MicroBotox) for the treatment of skin roughness and dryness on facial dermis.

Methods

Fifty women who had thin, dry skin with fine wrinkles throughout the whole face, especially in the crow’s feet and forehead areas, were enrolled in the study. Two cc stabilized-HA filler and 1 cc (40 U) of botulinumtoxinA were mixed in the novel combined hydrotoxin mixture. Intended to hydrate the dermis and treat fine wrinkles of the face, the mixture was injected into the real dermal layer of the face. The volume of HA per site was 0.002 cc and toxin was 0.04 U. Skin roughness and stratum corneum hydration were measured at 1, 2, 3, and 6 months.

Results

One month post-treatment, skin roughness was reduced to 50.19% in topographic computer analysis utilizing 10× dermascope photos. Stratum corneum hydration on crow’s feet improved to 81.34% at 1 month and 56.12% at 2 months from pre-treatment baseline (P < 0.0001). Global Aesthetic improvement scale of Skin hydration and fine wrinkle improved.

Conclusions

The combination injection method of MicroHA and MicroBotox is not associated with side effects and showed significant synergic effect in improvement of skin roughness and moisturizing. Neuramix-hydrotoxin injection method is an easy and reproducible procedure to make constant injection depth and amount.

Level of Evidence: 4
Deep learning meets metabolomics: a methodological perspective
Authors: Sen Partho , Lamichhane Santosh , Mathema Vivek B , McGlinchey Aidan , Dickens Alex M , Khoomrung Sakda , Orešič Matej
Published: August 2020

Deep learning (DL), an emerging area of investigation in the fields of machine learning and artificial intelligence, has markedly advanced over the past years. DL techniques are being applied to assist medical professionals and researchers in improving clinical diagnosis, disease prediction and drug discovery. It is expected that DL will help to provide actionable knowledge from a variety of ‘big data’, including metabolomics data. In this review, we discuss the applicability of DL to metabolomics, while presenting and discussing several examples from recent research. We emphasize the use of DL in tackling bottlenecks in metabolomics data acquisition, processing, metabolite identification, as well as in metabolic phenotyping and biomarker discovery. Finally, we discuss how DL is used in genome-scale metabolic modelling and in interpretation of metabolomics data. The DL-based approaches discussed here may assist computational biologists with the integration, prediction and drawing of statistical inference about biological outcomes, based on metabolomics data.
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses
Authors: Ciccolella Simone , Ricketts Camir , Soto Gomez Mauricio , Patterson Murray , Silverbush Dana , Bonizzoni Paola , Hajirasouliha Iman , Della Vedova Gianluca
Published: August 2020

Motivation

In recent years, the well-known Infinite Sites Assumption has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progressions. However, recent studies leveraging single-cell sequencing (SCS) techniques have shown evidence of the widespread recurrence and, especially, loss of mutations in several tumor samples. While there exist established computational methods that infer phylogenies with mutation losses, there remain some advancements to be made.

Results

We present Simulated Annealing Single-Cell inference (SASC): a new and robust approach based on simulated annealing for the inference of cancer progression from SCS datasets. In particular, we introduce an extension of the model of evolution where mutations are only accumulated, by allowing also a limited amount of mutation loss in the evolutionary history of the tumor: the Dollo-k model. We demonstrate that SASC achieves high levels of accuracy when tested on both simulated and real datasets and in comparison with some other available methods.

Availability and implementation

The SASC tool is open source and available at https://github.com/sciccolella/sasc.

Supplementary information

Supplementary data are available at Bioinformatics online.
Highly Sensitive Quantification of Plasma Severe Acute Respiratory Syndrome Coronavirus 2 RNA Sheds Light on its Potential Clinical Value
Authors: Veyer David , Kernéis Solen , Poulet Geoffroy , Wack Maxime , Robillard Nicolas , Taly Valérie , L’Honneur Anne-Sophie , Rozenberg Flore , Laurent-Puig Pierre , Bélec Laurent , Hadjadj Jérôme , Terrier Benjamin , Péré Hélène
Published: August 2020

Background

Coronavirus disease 2019 (COVID-19) is a global public health problem that has already caused more than 662 000 deaths worldwide. Although the clinical manifestations of COVID-19 are dominated by respiratory symptoms, some patients present other severe damage such as cardiovascular, renal and liver injury, and/or multiple organ failure, suggesting a spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in blood. Recent ultrasensitive polymerase chain reaction (PCR) technology now allows absolute quantification of nucleic acids in plasma. We intend to use the droplet-based digital PCR technology to obtain sensitive detection and precise quantification of plasma SARS-CoV-2 viral load (SARS-CoV-2 RNAemia) in hospitalized COVID-19 patients.

Methods

Fifty-eight consecutive COVID-19 patients with pneumonia 8 to 12 days after onset of symptoms and 12 healthy controls were analyzed. Disease severity was categorized as mild to moderate in 17 patients, severe in 16, and critical in 26. Plasma SARS-CoV-2 RNAemia was quantified by droplet digital Crystal Digital PCR next-generation technology (Stilla Technologies, Villejuif, France).

Results

Overall, SARS-CoV-2 RNAemia was detected in 43 (74.1%) patients. Prevalence of positive SARS-CoV-2 RNAemia correlated with disease severity, ranging from 53% in mild-to-moderate patients to 88% in critically ill patients (P = .036). Levels of SARS-CoV-2 RNAemia were associated with severity (P = .035). Among 9 patients who experienced clinical deterioration during follow-up, 8 had positive SARS-CoV-2 RNAemia at baseline, whereas only 1 critical patient with undetectable SARS-CoV-2 RNAemia at the time of analysis died at day 27.

Conclusion

SARS-CoV-2 RNAemia measured by droplet-based digital PCR constitutes a promising prognosis biomarker in COVID-19 patients.
YQFC: a web tool to compare quantitative biological features between two yeast gene lists
Authors: Wu Wei-Sheng , Wang Lai-Ji , Yen Han-Chen , Tseng Yan-Yuan
Published: August 2020

Nowadays high-throughput omics technologies are routinely used in biological research. From the omics data, researchers can easily get two gene lists (e.g. stress-induced genes vs. stress-repressed genes) related to their biological question. The next step would be to apply enrichment analysis tools to identify distinct functional/regulatory features between these two gene lists for further investigation. Although various enrichment analysis tools are already available, two challenges remain to be addressed. First, most existing tools are designed to analyze only one gene list, so they cannot directly compare two gene lists. Second, almost all existing tools focus on identifying the enriched qualitative features (e.g. gene ontology [GO] terms, pathways, domains, etc.). Many quantitative features (e.g. number of mRNA isoforms of a gene, mRNA half-life, protein half-life, transcriptional plasticity, translational efficiency, etc.) are available in the yeast, but no existing tools provide analyses on these quantitative features. To address these two challenges, here we present Yeast Quantitative Features Comparator (YQFC) that can directly compare various quantitative features between two yeast gene lists. In YQFC, we comprehensively collected and processed 85 quantitative features from the yeast literature and yeast databases. For each quantitative feature, YQFC provides three statistical tests (t-test, U test and KS test) to test whether this quantitative feature is statistically different between the two input yeast gene lists. The distinct quantitative features identified by YQFC may help researchers to study the underlying molecular mechanisms that differentiate the two input yeast gene lists. We believe that YQFC is a useful tool to expedite the biological research that uses high-throughput omics technologies.

Database URL

http://cosbi2.ee.ncku.edu.tw/YQFC/
A randomized controlled trial comparing controlled reoxygenation and standard cardiopulmonary bypass in paediatric cardiac surgery
Authors: Caputo Massimo , Scott Lauren J , Deave Toity , Dabner Lucy , Parry Andrew , Angelini Gianni D , Sheehan Karen , Stoica Serban , Ellis Lucy , Harris Rosie , Rogers Chris A
Published: August 2020

OBJECTIVES

Controlled reoxygenation on starting cardiopulmonary bypass (CPB) rather than hyperoxic CPB may confer clinical advantages during surgery for congenital cyanotic heart disease.

METHODS

A single-centre, randomized controlled trial was carried out to compare the effectiveness of controlled reoxygenation (normoxia) versus hyperoxic CPB in children with congenital cyanotic heart disease undergoing open-heart surgery (Oxic-2). The co-primary clinical outcomes were duration of inotropic support, intubation time and postoperative intensive care unit (ICU) and hospital stay. Analysis of the primary outcomes included data from a previous trial (Oxic-1) conducted to the same protocol.

RESULTS

Ninety participants were recruited to Oxic-2 and 79 were recruited to the previous Oxic-1 trial. There were no significant differences between the groups for any of the co-primary outcomes: inotrope duration geometric mean ratio (normoxia/hyperoxic) 0.97, 95% confidence interval (CI) (0.69–1.37), P-value = 0.87; intubation time hazard ratio (HR) 1.03, 95% CI (0.74–1.42), P-value = 0.87; postoperative ICU stay HR 1.14 95% CI (0.77–1.67), P-value = 0.52, hospital stay HR 0.90, 95% CI (0.65–1.25), P-value = 0.53. Lower oxygen levels were successfully achieved during the operative period in the normoxic group. Serum creatinine levels were lower in the normoxic group at day 2, but not on days 1, 3–5. Childhood developmental outcomes were similar. In the year following surgery, 85 serious adverse events were reported (51 normoxic group and 34 hyperoxic group).

CONCLUSIONS

Controlled reoxygenation (normoxic) CPB is safe but with no evidence of a clinical advantage over hyperoxic CPB.

Clinical trial registration number

Current Controlled Trials—ISRCTN81773762.
Review of the direct and indirect effects of warming and drought on scale insect pests of forest systems
Authors: Frank Steven D
Published: August 2020

Higher temperatures and drought are key aspects of global change with the potential to alter the distribution and severity of many arthropod pests in forest systems. Scale insects (Hemiptera: Coccoidea) infest many tree species and are among the most important pests of trees in urban and rural forests, plantations and other forest systems. Infestations of native or exotic scale insects can kill or sicken trees with economic and ecosystem-wide consequences. Warming can have direct effects on the life history, fitness and population dynamics of many scale insect species by increasing development rate, survival or fecundity. These direct benefits can increase the geographic distribution of scale insects and their consequences for tree health. Warming and drought can affect scale insects indirectly by altering the quality of their host trees. Additive or interactive effects of warming and drought can change tree quality in such a way that it increases scale insect fitness and population growth. However, the effects are species- and context-dependent with some scale insect species negatively affected by drought-induced changes in tree quality. Warming and drought are often coincident in urban forests and predicted to co-occur in many parts of the world under climate change scenarios. The individual and interactive effects of these factors require further research to inform predictions and management of scale insect pests. Warming also indirectly affects scale insects by altering interactions with natural enemies. This includes changes in natural enemy phenology, community composition and abundance. In addition, warming can alter scale insect phenology or voltinism causing asynchrony with natural enemies or population growth too rapid for natural enemies to suppress. Direct and indirect effects of warming and drought on scale insects can increase the potential for some exotic species to become established and for some native species to become invasive. Unfortunately, much research on scale insects is confined to a few particularly important native or exotic pests which limits our ability to predict the effects of warming on many current or potential pests. More research is required to understand how warming and drought affect scale insects, scale insect management and the forest systems they inhabit.
Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy
Authors: Aadland Kelsey , Kolaczkowski Bryan
Published: August 2020

Ancestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a phylogeny describing the history of the protein family and a model of the molecular-evolutionary process to infer the sequences of ancient proteins, allowing researchers to directly investigate the impact of sequence evolution on protein structure and function. Like all statistical inferences, ASR can be sensitive to violations of its underlying assumptions. Previous studies have shown that, whereas phylogenetic uncertainty has only a very weak impact on ASR accuracy, uncertainty in the protein sequence alignment can more strongly affect inferred ancestral sequences. Here, we show that errors in sequence alignment can produce errors in ASR across a range of realistic and simplified evolutionary scenarios. Importantly, sequence reconstruction errors can lead to errors in estimates of structural and functional properties of ancestral proteins, potentially undermining the reliability of analyses relying on ASR. We introduce an alignment-integrated ASR approach that combines information from many different sequence alignments. We show that integrating alignment uncertainty improves ASR accuracy and the accuracy of downstream structural and functional inferences, often performing as well as highly accurate structure-guided alignment. Given the growing evidence that sequence alignment errors can impact the reliability of ASR studies, we recommend that future studies incorporate approaches to mitigate the impact of alignment uncertainty. Probabilistic modeling of insertion and deletion events has the potential to radically improve ASR accuracy when the model reflects the true underlying evolutionary history, but further studies are required to thoroughly evaluate the reliability of these approaches under realistic conditions.
Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli
Authors: Batarseh Tiffany N , Hug Shaun M , Batarseh Sarah N , Gaut Brandon S
Published: August 2020

Evolutionary rescue occurs when adaptation restores population growth against a lethal stressor. Here, we studied evolutionary rescue by conducting experiments with Escherichia coli at the lethal temperature of 43.0 °C, to determine the adaptive mutations that drive rescue and to investigate their effects on fitness and gene expression. From hundreds of populations, we observed that ∼9% were rescued by genetic adaptations. We sequenced 26 populations and identified 29 distinct mutations. Of these populations, 21 had a mutation in the hslVU or rpoBC operon, suggesting that mutations in either operon could drive rescue. We isolated seven strains of E. coli carrying a putative rescue mutation in either the hslVU or rpoBC operon to investigate the mutations’ effects. The single rescue mutations increased E. coli’s relative fitness by an average of 24% at 42.2 °C, but they decreased fitness by 3% at 37.0 °C, illustrating that antagonistic pleiotropy likely affected the establishment of rescue in our system. Gene expression analysis revealed only 40 genes were upregulated across all seven mutations, and these were enriched for functions in translational and flagellar production. As with previous experiments with high temperature adaptation, the rescue mutations tended to restore gene expression toward the unstressed state, but they also caused a higher proportion of novel gene expression patterns. Overall, we find that rescue is infrequent, that it is facilitated by a limited number of mutational targets, and that rescue mutations may have qualitatively different effects than mutations that arise from evolution to nonlethal stressors.
‘It’s kinda bad, honestly’: Australian students’ experiences of relationships and sexuality education
Authors: Waling Andrea , Bellamy Roz , Ezer Paulina , Kerr Lucille , Lucke Jayne , Fisher Christopher
Published: August 2020

Relationships and sexuality education for young people in Australia and elsewhere is a controversial topic. Numerous studies in Australia have focused on curriculum, policy, teachers, schools, sexting and other behaviours, and knowledge regarding sexually transmitted infection (STI)/human immunodeficiency virus (HIV) and pregnancy prevention. Few large-scale national studies have engaged with young people about what they want out of their sex education, and what they suggest would be most valuable for future programs in Australia. Data for the study included qualitative comments about experiences of sex education (n = 2316) provided in a national survey of adolescent sexual health. An initial thematic inductive analysis identified comments falling into two dominant themes: positive and negative experiences of their sex education. Results indicate that young people in Australia are articulate and understanding of the gaps in their sex education. A majority of comments highlighted negative experiences. These comments primarily discussed issues of delivery (timing, environment, person) and content quality (comprehensiveness). A minority highlighted positive commentary also around delivery (environment, person) and content quality (comprehensiveness). The findings of this study illuminate contemporary adolescent concerns regarding their experiences of education. Understanding these experiences can inform future curriculum development, teacher training and the design and implementation of policy.
Quantifying the performance of selective devices by combining analysis of catch data and fish behaviour observations: methodology and case study on a flatfish excluder
Authors: Santos Juan , Herrmann Bent , Stepputtis Daniel , Kraak Sarah B M , Gökçe Gökhan , Mieske Bernd
Published: August 2020

This article describes a method for the quantitative analysis of fish behaviour relative to selection devices in trawl gears. Based on video observations, the method estimates probabilities for a given event to happen and establishes behavioural tree diagrams representing and quantifying behavioural patterns in relation to the selection device under assessment. Double bootstrapping is used to account for the uncertainty originating from a limited number of fish observations and the natural variation in fish behaviour. The method is used here to supplement standard analysis of catch data for the performance assessment of a flatfish excluder (FLEX). The Baltic Sea trawl fishery targeting cod (Gadus morhua) provides the pilot case. Results obtained by comparing catches with and without FLEX installed revealed that >75% of bycaught flatfish individuals escaped through the device, while no evidence was found that catches of cod in the targeted sizes were reduced. The behavioural analysis produced values of escape efficiency comparable to those obtained in the catch analysis. Furthermore, it revealed that ∼80% of the flatfish went calmly into the excluder, while most of the roundfish displayed avoidance swimming reactions. The method provides quantitative information of fish behaviour that can be relevant for developing and optimizing selection devices.