bluuebunny/crossref_metadata_2025 huggingface dataset:
The utilization of gypsum board and fly ash waste on brick in terms of compressive strength to reduce environmental pollution
Authors: Taveriyanto A , Andiyarto H T C , Saefullah M V , Haliza M P
Published: February 2022

The utilization of gypsum board and fly ash waste as alternative materials in making bricks is one of the efforts to reduce the amount of industrial waste in the construction sector, namely gypsum board and fly ash waste. The use of gypsum board and fly ash waste cannot be separated from relatively large amount and the potential to pollute the environment. The pozzolanic properties contained in fly ash combined with gypsum board waste are expected to improve the quality of the bricks. The purpose of this study was to determine the value of the compressive strength of bricks. The method used is an experimental research method in which variations in the composition of gypsum board and fly ash waste are 0% and 0%, 5% and 25%, 7.5%, and 27.5%, and 10% and 30% of the weight, respectively. cement using a sample size of 37 x 10 x 15 cm. Based on the results of the study, it showed that the compressive strength test of the gypsum board and fly ash waste bricks had met the quality requirements according to SNI 03-0349-1989 with the average compressive strength value for each composition of 42.37 Kg/cm2, 73.04 Kg/cm2, 49.30 Kg/cm2, and 43.59 Kg/cm2.
Design and static testing of electric vehicle chassis trike front-wheel drive
Authors: Aryadi W , Setiyawan A , Kriswanto  , Rizky A
Published: February 2022

Compared to conventional vehicles, the advantages of electric vehicles are more significant acceleration, no exhaust emissions, making electric vehicles more environmentally friendly, minimal maintenance because there are not many components used in electric cars. This research method is used to develop the chassis design of an electric trike, and then the chassis design is analysed using Solidworks software. The chassis with a thickness of 2.4 mm weights 29.6 kg with a maximum value of stress, displacement, strain, and other factors. Safety as follows: 7,582 x 107 N/m2, 2,567 mm, 3,368 10−4 and 3.5, 2 mm thick chassis weighs 25 kg with maximum stress, displacement, strain, and safety factor values as follows: 1.079x108 N/m2, 3.160 mm, 3.981 10−4 and 2.5 then the chassis thickness of 1.6 mm weights 20.3 kg with the maximum stress, displacement, strain, and safety factor values as follows: 1.809 x 108 N/m2, 4.190 mm, and 9.388 10−4. Chassis with a thickness of 2 mm using a rectangular tube and ASTM A53 material has a safety factor value that is by the requirements and the maximum stress value on the chassis does not exceed the allowable stress value and weight.
Development of a power breaker system in small-scale wind power plants when there is high rotation (over speed)
Authors: Ananta H , Murnomo A , Isdiyarto  , Sunardiyo S , Pridayanto S B P , Nurmaulida I
Published: February 2022

In a wind power plant (hereinafter referred to as PLTB), rotation stability is needed, to protect the system from sudden rising and unpredictable wind speed. Large-scale PLTBs are already equipped with a braking system, unlike small-scale plants that are generally not equipped with a braking system. In order for the electricity supply to be guaranteed properly and for the system to be protected, it is necessary to make a control device that will monitor the rotation speed of the generator and turn off the electricity supply to the system should there be any rotation that exceeds the specified limit / over speed. The use of small-scale for household purposes is generally equipped with an electric power storage / battery and an inverter to convert DC electricity into AC electricity which is then used by consumers. This research uses the research and development approach, namely research that will produce an effective and efficient power breaker system as a function of creation and innovation in solving renewable energy problems. Result; the automatic power breaker suitable for use in small-scale wind power plant has been assembled and tested with good results and is ready for use.
Diesel engine performance test using solar-dex and biodiesel (B30) on power and torque
Authors: Setiyawan A , Novianto A , Afkar N B A , Chabib F , Amelia F R , Pratiwi I
Published: February 2022

Biodiesel as renewable alternative energy produced from vegetable and animal oils can be used to fuel diesel engines. Pertamina has officially release Biodiesel B30, which sells on fuel stations in Indonesia. The purpose of this study is to investigate the diesel engine performance on Solar-Dex and Biodiesel blend. Testing the performance of a diesel engine by mixing Solar-Dex and Biodiesel on power and torque produces different data and can be concluded: (1) Pure Solar-Dex without the addition of Biodiesel gives the lowest power yield of 49.55 kW, while the data fluctuates when adding Biodiesel and it is known that the most considerable average power occurs when a mixture of Biodiesel is 30% with 70 Solar-Dex and 40% biodiesel with 60% Solar-Dex which is 54 kW. (2) Pure Solar-Dex without the addition of bio-diesel gives the lowest torque yield of 120.45 Nm, while the data fluctuates when adding Biodiesel and it is known that the most considerable average torque occurs when a mixture of 20% bio-diesel with 80 Solar-Dex is 122, 8 Nm.
Quality test of current catfish nuggets in improving children’s health
Authors: Widayani S , Darmi T , Agustina T , Astuti R M , Elvita D , Aini N , Dewantara A
Published: February 2022

The covid-19 pandemic had the greatest impact on public health. The pandemic period has not ended and is still haunting the community. To maintain life, people must continue to do activities in meeting the nutritional needs of their families to be healthy so as to avoid the covid-19 virus. The impact of covid-19, more than 20% of children under five are malnourished. The pandemic condition has stirred and stirred the hearts of the research team to try out today’s nutritious processed food for children to improve their health. It is suspected that the provision of food can contribute to the protein sufficiency of children under five years old. Hope that adequacy consumption of nuggets can improve health because they are used as snacks or side dishes. Therefore, the quality test of nugget products is very necessary. The research objectives were to: 1) study the quality of nuggets, and 2) determine the health level of children under five. Completely randomized design (CRD) method for product quality. Pure experiment with randomized control trial design on children under five in Gunungpati area purposively on nugget intervention was done. Anamnesis method was carried out to explore children’s health and anthropometry with TB/U index to determine nutritional status. The study used 10 semi-expert panellists and 30 children under five years old. The results showed that nuggets were widely liked by children. Catfish nuggets can improve the health of children (p<0.05).
Natural food colourant of beetroot skin (Beta vulgaris L): characterisation study
Authors: Paramita O , Ansori M , Kusumastuti A , Fatimah N
Published: February 2022

The culinary industry is now growing, where the use of food colourant is widely used as an additive. To produce attractive colours in food, many manufacturers use synthetic colourant. The use of synthetic colourant will endanger health because synthetic colourant contains heavy metals. Supports UNNES vision, which is to become a conservation-minded university. In this study, the theme of the use of waste, especially fruit skin waste, as a natural colourant that is safe for health. The types of natural colourant that are often used for colourant are betacyanin. Fruit skin waste contains a lot of natural colourant, including beetroot skin. The results showed that the appropriate extraction method was the maceration method with the results for beetroot colourant resulting in the most optimal water content, antioxidant content and colour in the dye using a single solvent in the form of Ethanol.
Preparation and characterization of binahong (Anredera cordifolia) leaves extract-based liquid hand soap
Authors: Megawati  , Imani N A C , Fardhyanti D S , Astuti W , Hadikawuryan D S
Published: February 2022

The need for hand soap is increasing along with the increase of public awareness to maintain cleanliness and health. Commercial hand soaps are made from various chemical mixtures which often give side effects in the form of allergies in people who have sensitive skin. The production of soap with natural ingredients can be a way to solve these problems. In this paper, we report an observational study of the effect of adding binahong leaf oil extract, which is known to have antiseptic properties and is often used as an itching remedy, on the characteristics of liquid hand soap. The research was carried out with the steps of preparation of binahong leaf, binahong leaf oil extract, and production of soap based-binahong leaf extract oil with various concentrations of mixing ingredients. The analysis carried out in this experiment were the analysis of physical and chemical properties as well as the effectiveness of the soap against bacteria after the use of the liquid hand soap. The addition of binahong leaf extract oil in the liquid hand soap can increase the antibacterial properties of the liquid hand soap and has the potential to be used as a soap that is safer for daily use.
Ternary liquid-liquid equilibrium for eugenol + tert-butanol + water and eugenol + 1-octanol + water systems at 303.15 K and atmospheric pressure
Authors: Sucipto R K H , Kuswandi K , Wibawa G
Published: February 2022

The objective of this work was to determine ternary liquid-liquid equilibrium for eugenol + tert-butanol + water and eugenol + 1-octanol + water systems at 303.15K and atmospheric pressure. The experimental apparatus was 25 mL equilibrium cell equipped jacketed water connected to water bath to maintain equilibrium temperature at constant value. The procedure of this experiment was conducted by inserting mixture of eugenol + tert-butanol + water and eugenol + 1-octanol + water systems at certain composition into equilibrium cell. The solution was stirred for 4 hours and then was allowed for 20 hours in order to separate aqueous and organic phases completely. The equilibrium compositions of each phase were analysed using gas chromatography. The experimental data obtained in this work were correlated with NRTL and UNIQUAC models giving root standard mean deviation of 1.1% and 1.5%, respectively for eugenol + tert-butanol + water system and that of 2.8 % and 3.1%, respectively for eugenol + 1-octanol + water system. 1-octanol which has better capability than tert-butanol as a solvent for eugenol.
Microcontroller-based supporting tool for socializing in physical distancing during Covid-19 pandemic
Authors: Sanjaya Z N , Utomo A B
Published: February 2022

Physical distancing is one of the procedures to avoid the spread of Covid-19. Several researchers have created tools to support physical distancing and the detection focus is on the front or back side with sound alert. However, this kind of sound alert can disturb other people activities. Moreover, people have a blind spot in their right and left side vision which is more than 400 on the horizontal plane. The study aims to design two bracelets for socializing in physical distancing during Covid-19 pandemic. It works at a distance of 1 meter within a radius of 1200 on eye blind spot and provide the option of a vibration or sound alert or both with the push button. The main components of this tool are Arduino nano as the system controller, HC-SR 04 ultrasonic sensor as the distance measure, PIR HC-SR 501 sensor as the people movement detection, continuous rotation servo motor MG90S as the sensors driver of 1200, vibrating DC motor type 310-101 as the vibration output and buzzer as the sound output. The result of this study is two bracelets that available to detect distance and movement on the 1200 rotation angle. When both of bracelets on the 1-meter distance, they will make vibration, sound, or both.
Spatial patterns of settlements in the Menara Kudus Mosque area
Authors: Nila S A E , Marlina A , Winarto Y
Published: February 2022

The settlement in the Menara Kudus Mosque area is a catalyst for religious tourism activities that are adjacent to the residence of the local community. Menara Kudus Mosque with its own characteristics will have an impact on changes that occur both physically and non-physically. This study aims to further identify the formation of the spatial patterns of settlements in the Menara Kudus Mosque area caused by the exposure of religious tourism. The spatial patterns that occur can be seen through observations on the layout, circulation, facing direction, and hierarchy. In this study of the spatial pattern of the Menara Kudus Mosque settlement, the researcher used a messo (residential environment), micro (residential) scale coverage and the factors behind it. The research method for data analysis used in this research is descriptive qualitative with a case study strategy in the residential area of Menara Kudus Mosque. The results of this study indicate that the existing spatial pattern is the result of a response to the new activities of the surrounding community which utilize their residential space and their residential environment as a business space that supports religious tourism activities.
Building design recommendation for thermal comfort in cities on the island of Java, Indonesia
Authors: Setiawan M F
Published: February 2022

Thermal comfort is a person’s state of mind that expresses a person’s level of satisfaction with his environment. Optimal thermal comfort can be achieved by considering several factors, including building orientation, air conditioning, position and size of openings, building materials, and others. The purpose of this study is to find recommendations for designing thermal comfort in cities on the island of Java using Mahoney Tables. Mahoney Tables is a collection of reference tables used in construction as climate-friendly design references. In this study, climate and meteorological data will be taken in certain cities on the island of Java. From the results of the above discussion, it can be concluded that the building must pay attention to 4 aspects, namely openings, the building must have wide openings located on the south-north side of the building and the openings must be as high as the human body; The room must be one room without a partition; Building envelopes, buildings must be protected from direct sunlight and rain by paying attention to the selection of materials; and building utilities must pay attention to drainage. The recommendations above are expected to be used by architects/researchers who will design/research buildings to be comfortable.
Behaviour analysis of building column structure with retaining wall due to explosion load in front and side a construction
Authors: Pangestuti E K , Kamilah N H
Published: February 2022

Analysis of the impact of explosion loads on buildings to determine the structural column reaction conditions as a result of the blast loads. The model building structure is a three-story structure with a height of 10.5 meters. At distances between 10 and 15 meters from the source of the blast, the analysed explosive weight of 500 kg TNT was converted to a static load. SAP2000 software was used to conduct the analysis. The analyses’ results in the form of a moment force that compares a building’s column structure’s response. Based on this analysis, it can be concluded that the conditions in the structure without restrained walls are insufficient to withstand the blast load, while the structure with restrained walls is capable of receiving explosive loads.
The mitigation of Covid-19 in the perspective of contractor for sustainable construction in Indonesia
Authors: Fauziyah S , Susanti R , Lukman
Published: February 2022

Construction has been significantly influenced by COVID-19. In some countries, construction projects are discontinued, and even in some countries where construction work is still permitted, high safety standards are required. Construction site safety is essential during the COVID-19 pandemic. The contractor is responsible for creating a safe workplace at the project site. Therefore, this paper presents project risk identification and mitigation during the covid-19 pandemic based on contractor’s perspective. This research identified the risk factors related to the COVID-19 pandemic that consist of 5 categories: man, materials, machines, methods, and environment. Between these risk factors, worker shortage, site accessibility, and lack of construction materials, caused by the strict large-scale social restrictions (PSBB) policy are the biggest challenges faced by the contractor. The findings of this research develop the project risk categories and mitigation strategies from the contractor’s perspective. It suggests that future construction in addition to planning the design, operate, maintenance, supply chain, and project management must also consider the occurrence of a pandemic.
The dynamics of the factory function as a production room at the house of clothing artisans in Pekalongan
Authors: Wibowo A A , Setyohadi B , Wicaksono D
Published: February 2022

Technological innovation provides many business opportunities (technopreneurs) that involve various fields of study. Architecture is not an exception; technological advances can create a “hi-tech” masterpiece. There are two fields of study related to the application of architectural technology. First, the use of technology to improve the quality of architectural products, so that the design results are considered to be able to keep up with the times, such as materials and technological elements. Second, a form of architectural preservation that can be used as a guide in following technological developments, such as spatial planning. During the Diponegoro War some of his followers were forced to leave Mataram, then those who stopped in Pekalongan began to introduce batik in three areas: Wonopinggo, Pekajangan, and Buaran in 1825-1830. Gradually, batik production increased, until it is expanded into weaving craft. Both types of clothing production can’t be separated from technological advances, handmade batik is replaced with stamped batik, and the weaving of ATBM production changes to using ATMs. The historical journey that transformed Pekalongan as a well-known clothing city in Indonesia is interesting to study, especially in the architectural field, namely spatial planning formed from local culture. This study discusses the spatial preservation of clothing production houses in three areas in Pekalongan, namely: Pekajangan, Kauman, and Pesindon. The objective of the study was to identify the form of spatial preservation used during the development of clothing-making technology. Descriptive-exploratory research method is used to explore elements of local wisdom used as guidelines for spatial planning. The results of the study elaborate that the layout of the clothing production house in Pekajangan, Kauman, and Pesindon consists of: living room, family room, drying room, and factory. However, there are differences in the location of the drying room. This difference is due to the change in function from residential building to production building, and also from the development of clothing technology. This requires some additional spaces. Based on the research results from the three areas, the factory is a long-lasting and sustainable space category.
Youth social behaviour in using the city’s public space (case study of Menteng Bintaro park)
Authors: Purnomo A
Published: February 2022

The Menteng Bintaro park is one of the city parks available in South Tangerang City. This city park is one of the destinations frequently visited by the community, especially teenagers. Social behaviour commonly owned by adolescents is usually characterized by the tendency of adolescents to try to separate themselves from parental supervision where adolescents tend to have a desire to be free, but not infrequently adolescent behaviour leads to deviant behaviour patterns. As a public facility, a city park must of course provide comfort for everyone who visits it. So, it is necessary to make observations about the social behaviour of adolescents in using city parks as public spaces. This research objective was to evaluate the social behaviour of adolescents in using urban public spaces with details including: identifying forms of adolescent social behaviour in utilizing city parks; evaluating the existing condition of the city park; identify the factors that influence the use of Menteng Bintaro park by youth. The object of research is Menteng Bintaro Park which is located in Sector 7 Bintaro Jaya, Jl. Wahid Hasyim, Pondok Jaya, Kecamatan Pondok Aren, South Tangerang City, Banten. This study uses descriptive qualitative methods with data collection techniques including observation and documentation. The data analysis technique used in this research is descriptive qualitative.
Modelling student travel mode choice: a case study in Semarang, Indonesia
Authors: Haryadi B , Narendra A , Purnomo M , Purnomo A
Published: February 2022

The paper presents an investigation of university students’ travel mode choice behaviour for commuting to campus. It uses a dataset collected through a survey among students of four universities in Semarang, i.e., Unnes, UINW, Udinus, and Unissula. Eight hundred and thirty-seven respondents completed the questionnaires. Multinomial logit (MNL) models are used for investigating four transport mode choices, i.e., walk, motorcycle, car, and bus. The independent variables are schools, genders, origin, residential types, vehicle ownership, driving license ownership, monthly allowance, transportation budget, and commuting distance. The model shows that all independent variables, except monthly allowance, are significant predictors. Overall, the model prediction accuracy is about 90 percent. A motorcycle was the foremost prevalent transport for school trips. Empirical models reveal that the mode of choice behaviour of non-native students differs significantly from those that originate in Semarang. The log odds of driving a car, riding a motorcycle, and walking versus riding a bus are higher when students’ origin is not from Semarang compared to Semarang.
Comparison of retrofit failure to pull out single anchor of plain steel and deformed cast inplace and post installed chemical epoxy methods
Authors: Apriyatno H , Supriyono  , Sutarto A , Hanggoro
Published: February 2022

One of the anchor functions is to connect the construction steel joint to the concrete to transfer the tensile force of steel to concrete. The research aimed to compare the theoretical and experimental adhesive stress and the pullout capacity of plain steel single anchors and deformed cast in place and retrofit post-installed chemical epoxy sika anchor fix-2. The experimental result of the cast in place method of the plain steel anchors to the theoretical increase by 3.657% and deformed steel anchor increased by 50.13%; retrofit post-installed chemical epoxy sika anchor fix-2 method of plain steel to the theoretical increased by 23.29% and deformed steel anchor increased 63.69% and plain steel anchor method and retrofit postinstalled chemical epoxy sika anchor fix-2 to the cast in place increased by 18.404% and steel anchor deform increased by 8.905%. Therefore, retrofit post-installed chemical epoxy sika anchor fix-2 plain anchor and deformed steel anchor give better results than cast in place theory so that the basis for the planning can be used as the basis for retrofit post-installed chemical epoxy sika anchor fix-2 while overall, deformed steel anchor is still better than plain steel anchor.
Transportation modelling using PTV Vissim for the adjacent junction in Sampangan Semarang City
Authors: Nugroho U , Falah K T
Published: February 2022

The growth of vehicles in the city of Semarang is fast, as calculated based on the BPS Semarang the number of vehicle growth is 11% per year. This causes the road capacity to be periodically increased. As is the case at the adjacent intersections on Dewi Sartika street and Talangsari street initially, to break up delays and queues and increase capacity, efforts were made to add a 7-meter-wide bridge. However, this widening will not solve the problem in the next 5 years so that alternative solutions are needed for the two intersections. This study aims to evaluate the two intersections using the Binamarga method based on the 1993 MKJI, to determine the capacity of the intersection and plan the design of the intersection in the future and then make modelling with PTV Vissim Software to describe the simulation of the actual situation.
The role of asymmetry in few-cycle, mid-IR pulses during THz pulse generation
Authors: Flender Roland , Borzsonyi Adam , Chikan Viktor
Published: February 2022

The efficiency of terahertz (THz) pulse generation improves at longer driving wavelengths. For this reason, the use of mid-infrared (MIR) sources is more advantageous compared to visible or near-infrared systems. In this work, we investigate how single-color and two-color schemes of MIR pulses with few-cycle pulse durations compare in producing THz pulses. The results reveal that as the duration of the driving pulses decreases, the second harmonic generation crystal can be omitted from the system. Our numerical study pinpointed three regions where the optimal pulse parameters are fundamentally different for the most efficient THz pulse generation. The first is the two-color approach, where the two-color scheme is dominant at 3.2 optical cycles and over. The second is the single-color approach, where the single-color scheme becomes dominant at 1.7 optical cycles and below. Therefore, it simplifies the traditional two-color scheme for THz pulse generation. There is also a third transitional region where the two-color scheme still prevails, but the sign of the relative phase between the input pulses becomes important. Considering the effect of the relative phase and the carrier to envelope phase (CEP) effect on the THz pulse generation, the results have shown that as the pulse duration become shorter, the role of the CEP becomes important for efficient THz generation. By measuring the efficiency of the THz generation in this optical arrangement, quantifying the CEP becomes possible, which could become an important experimental tool for few-cycle, MIR laser technology.
Quality enhancement and microbial reduction of mung bean (Vigna radiata) sprouts by non-thermal plasma pretreatment of seeds
Authors: CUI Dongjie , HU Xiaoxia , YIN Yue , ZHU Yupan , ZHUANG Jie , WANG Xiaojie , MA Ruonan , JIAO Zhen
Published: February 2022

Mung bean (Vigna radiata) sprouts are widely consumed worldwide due to their high nutritional value. However, the low yield and microbial contamination of mung bean sprouts seriously reduces their economic value. This study investigates the effects of non-thermal plasma on the quality and microbial reduction of mung bean sprouts by pretreatment of seeds in water for different times (0, 1, 3 and 6 min). The quality results showed that short-time plasma treatment (1 and 3 min) promoted seed germination and seedling growth, whereas long-time plasma treatment (6 min) had inhibitory effects. Plasma also had a similar dose effects on the total flavonoid and phenolic contents of mung bean sprouts. The microbiological results showed that plasma treatment achieved a reduction of native microorganisms ranging from 0.54 to 7.09 log for fungi and 0.29 to 6.80 log for bacteria at 96 h incubation. Meanwhile, plasma treatment could also efficiently inactivate artificially inoculated Salmonella typhimurium (1.83–6.22 log) and yeast (0.53–3.19 log) on mung bean seeds. The results of seed coat permeability tests and scanning electron microscopy showed that plasma could damage the seed coat structure, consequently increasing the electrical conductivity of mung bean seeds. The physicochemical analysis of plasma-treated water showed that plasma generated various long- and short-lived active species [nitric oxide radicals (NO·), hydroxyl radicals (·OH), singlet oxygen (1O2), hydrogen peroxide (H2O2), nitrate (

NO

3

−

), and nitrite (

NO

2

−

)] in water, thus the oxidizability, acidity and conductivity of plasma-treated water were all increased in a treatment time-dependent manner. The result for mimicked chemical mixtures confirmed the synergistic effect of activity of H2O2,

NO

3

−

and

NO

2

−

on bacterial inactivation and plant growth promotion. Taken together, these results imply that plasma pretreatment of mung bean seeds in water with moderate oxidizability and acidity is an effective method to improve the yield of mung bean sprouts and reduce microbial contamination.
Tensor quasi-random groups
Authors: Sellke Mark
Published: February 2022

Gowers [Combin. Probab. Comput. 17 (2008), pp. 363–387] elegantly characterized the finite groups

G
G

in which

A
1

A
2

A
3

=
G

A_1A_2A_3=G

for any positive density subsets

A
1

,

A
2

,

A
3

A_1,A_2,A_3

. This property, quasi-randomness, holds if and only if

G
G

does not admit a nontrivial irreducible representation of constant dimension. We present a dual characterization of tensor quasi-random groups in which multiplication of subsets is replaced by tensor product of representations.
A doubling of atmospheric CO2 mitigates the effects of severe drought on maize through the preservation of soil water
Authors: Ripley B S , Bopape T M , Vetter S
Published: February 2022

Background and Aims

Drought limits maize production in many regions of the world, and this is likely to intensify in future. Elevated atmospheric CO2 (eCO2) can mitigate this by reducing stomatal conductance and water loss without reducing yield. The magnitude of this effect depends on the interaction of eCO2 and drought severity, but scarce data collected under severe drought conditions limit predictions of future maize production.

Methods

We compared the severe drought × eCO2 responses of six maize genotypes from semi-arid and sub-humid growing regions.

Key Results

Genotypic differences were apparent in growth, gas exchange, water relations, grain quality, and biomass at maturity, but the response to eCO2 was consistent. Plants under drought and eCO2 had similar biomass and yield to irrigated plants at ambient CO2. Reduced stomatal conductance and water loss preserved soil moisture equivalent to 35 mm of rainfall and allowed sustained photosynthesis at higher rates for a longer period after watering stopped. Under irrigation, eCO2 improved maize growth but not grain yield.

Conclusions

The results suggest that eCO2 may extend the future land area available to rainfed maize cultivation, but cannot circumvent the absence of seasonal rainfall that restricts maize growth. Elevated CO2 will reduce water requirements of irrigated maize when atmospheric conditions drive high evapotranspiration.
Multiview network embedding for drug-target Interactions prediction by consistent and complementary information preserving
Authors: Shang Yifan , Ye Xiucai , Futamura Yasunori , Yu Liang , Sakurai Tetsuya
Published: February 2022

Accurate prediction of drug-target interactions (DTIs) can reduce the cost and time of drug repositioning and drug discovery. Many current methods integrate information from multiple data sources of drug and target to improve DTIs prediction accuracy. However, these methods do not consider the complex relationship between different data sources. In this study, we propose a novel computational framework, called MccDTI, to predict the potential DTIs by multiview network embedding, which can integrate the heterogenous information of drug and target. MccDTI learns high-quality low-dimensional representations of drug and target by preserving the consistent and complementary information between multiview networks. Then MccDTI adopts matrix completion scheme for DTIs prediction based on drug and target representations. Experimental results on two datasets show that the prediction accuracy of MccDTI outperforms four state-of-the-art methods for DTIs prediction. Moreover, literature verification for DTIs prediction shows that MccDTI can predict the reliable potential DTIs. These results indicate that MccDTI can provide a powerful tool to predict new DTIs and accelerate drug discovery.

The code and data are available at: https://github.com/ShangCS/MccDTI.
RF-Net 2: fast inference of virus reassortment and hybridization networks
Authors: Markin Alexey , Wagle Sanket , Anderson Tavis K , Eulenstein Oliver
Published: February 2022

Motivation

A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens.

Results

Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses.

Availability and implementation

RF-Net 2 is available at https://github.com/flu-crew/rf-net-2.

Supplementary information

Supplementary data are available at Bioinformatics online.
Evolution of cross-frequency coupling between endogenous oscillations over the temporal cortex in very premature neonates
Authors: Saadatmehr Bahar , Edalati Mohammadreza , Routier Laura , Mahmoudzadeh Mahdi , Safaie Javad , Kongolo Guy , Ghostine Ghida , Wallois Fabrice , Moghimi Sahar
Published: February 2022

Temporal theta activity in coalescence with slow-wave (TTA-SW) is one of the first neurobiomarkers of the neurodevelopment of perisylvian networks in the electroencephalography (EEG). Dynamic changes in the microstructure and activity within neural networks are reflected in the EEG. Slow oscillation slope can reflect synaptic strength, and cross-frequency coupling (CFC), associated with several putative functions in adults, can reflect neural communication. Here, we investigated the evolution of CFC, in terms of SW theta phase-amplitude coupling (PAC), during the course of very early development between 25 and 32 weeks of gestational age in 23 premature neonates. We used high-resolution EEG and dipole models as spatial filters to extract the source waveforms corresponding to TTA-SW. We also carried out nonlinear phase-dependent correlation measurements to examine whether the characteristics of the SW slopes are associated with TTA-SW coupling. We show that neurodevelopment leads to temporal accumulation of the SW theta PAC toward the trough of SW. Steepness of the negative going slope of SW determined the degree of this coupling. Systematic modulation of SW-TTA CFC during development is a signature of the complex development of local cortico-cortical perisylvian networks and distant thalamo-cortical neural circuits driving this nested activity over the perisylvian networks.
Biofilm and invertebrate consumption by western sandpipers (Calidris mauri) and dunlin (Calidris alpina)during spring migratory stopover: insights from tissue and breath CO2 isotopic (δ13C,δ15N) analyses
Authors: Hobson Keith A , Kuwae Tomohiro , Drever Mark C , Easton Wendy E , Elner Robert W
Published: February 2022

Shorebirds use key migratory stopover habitats in spring and fall where body proteins are replenished and lipids stored as fuel for the remaining journey. The Fraser River estuary, British Columbia, Canada, is a critical spring stopover site for hundreds of thousands of migrating western sandpiper, Calidris mauri, and dunlin, Calidris alpina. Intertidal biofilm in spring is an important nutritional source for western sandpiper, with previous isotopic research predicting 45–59% of total diet and 50% of total energy needs. However, these studies relied on isotopic mixing models that did not consider metabolic routing of key dietary macromolecules. Complexity arises due to the mixed macromolecular composition of biofilm that is difficult to characterize isotopically. We expanded on these earlier findings by considering a protein pathway from diet to the body protein pool represented by liver tissue, using a Bayesian mixing model based on δ13C and δ15N. We used δ13C measurements of adipose tissue and breath CO2 to provide an estimate of the carbohydrate and protein δ13C values of microphytobenthos and used these derived values to better inform the isotopic mixing models. Our results reinforce earlier estimates of the importance of biofilm to staging shorebirds in predicting that assimilated nutrients from biofilm contribute ~35% of the protein budgets for staging western sandpipers (n = 13) and dunlin (n = 11) and at least 41% of the energy budget of western sandpiper (n = 69). Dunlin’s ingestion of biofilm appeared higher than anticipated given their expected reliance on invertebrate prey compared to western sandpiper, a biofilm specialist. Isotopic analyses of bulk tissues that consider metabolic routing and that make use of breath CO2 and adipose lipid assays can provide new insights into avian physiology. We advocate further isotopic research to better understand biofilm use by migratory shorebirds in general and as a critical requirement for more effective conservation.
PSINDB: the postsynaptic protein–protein interaction database
Authors: Kalman Zsofia E , Dudola Dániel , Mészáros Bálint , Gáspári Zoltán , Dobson Laszlo
Published: February 2022

The postsynaptic region is the receiving part of the synapse comprising thousands of proteins forming an elaborate and dynamically changing network indispensable for the molecular mechanisms behind fundamental phenomena such as learning and memory. Despite the growing amount of information about individual protein–protein interactions (PPIs) in this network, these data are mostly scattered in the literature or stored in generic databases that are not designed to display aspects that are fundamental to the understanding of postsynaptic functions. To overcome these limitations, we collected postsynaptic PPIs complemented by a high amount of detailed structural and biological information and launched a freely available resource, the Postsynaptic Interaction Database (PSINDB), to make these data and annotations accessible. PSINDB includes tens of thousands of binding regions together with structural features, mediating and regulating the formation of PPIs, annotated with detailed experimental information about each interaction. PSINDB is expected to be useful for various aspects of molecular neurobiology research, from experimental design to network and systems biology-based modeling and analysis of changes in the protein network upon various stimuli.

Database URL

https://psindb.itk.ppke.hu/
Left atrial reservoir strain improves diagnostic accuracy of the 2016 ASE/EACVI diastolic algorithm in patients with preserved left ventricular ejection fraction: insights from the KARUM haemodynamic database
Authors: Venkateshvaran Ashwin , Tureli Hande Oktay , Faxén Ulrika Ljung , Lund Lars H , Tossavainen Erik , Lindqvist Per
Published: February 2022

Aims

This study aimed to investigate the incremental value offered by left atrial reservoir strain (LASr) to the 2016 American Society of Echocardiography/European Association of Cardiovascular Imaging (ASE/EACVI) diastolic algorithm to identify elevated left ventricular (LV) filling pressure in patients with preserved ejection fraction (EF).

Methods and results

Near-simultaneous echocardiography and right heart catheterization were performed in 210 patients with EF ≥50% in a large, dual-centre study. Elevated filling pressure was defined as invasive pulmonary capillary wedge pressure (PCWP) ≥15 mmHg. LASr was evaluated using speckle-tracking echocardiography. Diagnostic performance of the ASE/EACVI diastolic algorithm was validated against invasive reference and compared with modified algorithms incorporating LASr. Modest correlation was observed between E/e′, E/A ratio, and LA volume index with PCWP (r = 0.46, 0.46, and 0.36, respectively; P < 0.001 for all). Mitral e′ and TR peak velocity showed no association. The ASE/EACVI algorithm (89% feasibility, 71% sensitivity, 68% specificity) demonstrated reasonable ability (AUC = 0.69) and 68% accuracy to identify elevated LV filling pressure. LASr displayed strong ability to identify elevated PCWP (AUC = 0.76). Substituting TR peak velocity for LASr in the algorithm (69% sensitivity, 84% specificity) resulted in 91% feasibility, 81% accuracy, and stronger agreement with invasive measurements. Employing LASr as per expert consensus (71% sensitivity, 70% specificity) and adding LASr to conventional parameters (67% sensitivity, 84% specificity) also demonstrated greater feasibility (98% and 90%, respectively) and overall accuracy (70% and 80%, respectively) to estimate elevated PCWP.

Conclusions

LASr improves feasibility and overall accuracy of the ASE/EACVI algorithm to discern elevated filling pressures in patients with preserved EF.
Cereblon contributes to cardiac dysfunction by degrading Cav1.2α
Authors: Park Nammi , Marquez Jubert , Pham Trong Kha , Ko Tae Hee , Youm Jae Boum , Kim Min , Choi Seung Hak , Moon Jiyoung , Flores Jessa , Ko Kyung Soo , Rhee Byoung Doo , Shimizu Ippei , Minamino Tohru , Ha Jae Du , Hwang Jong Yeon , Yang Seung Joo , Park Chul-Seung , Kim Hyoung Kyu , Han Jin
Published: February 2022

Aims

Cereblon (CRBN) is a substrate receptor of the E3 ubiquitin ligase complex that was reported to target ion channel proteins. L-type voltage-dependent Ca2+ channel (LTCC) density and dysfunction is a critical player in heart failure with reduced ejection fraction (HFrEF). However, the underlying cellular mechanisms by which CRBN regulates LTCC subtype Cav1.2α during cardiac dysfunction remain unclear. Here, we explored the role of CRBN in HFrEF by investigating the direct regulatory role of CRBN in Cav1.2α activity and examining how it can serve as a target to address myocardial dysfunction.

Methods and results

Cardiac tissues from HFrEF patients exhibited increased levels of CRBN compared with controls. In vivo and ex vivo studies demonstrated that whole-body CRBN knockout (CRBN−/−) and cardiac-specific knockout mice (Crbnfl/fl/Myh6Cre+) exhibited enhanced cardiac contractility with increased LTCC current (I  CaL) compared with their respective controls, which was modulated by the direct interaction of CRBN with Cav1.2α. Mechanistically, the Lon domain of CRBN directly interacted with the N-terminal of Cav1.2α. Increasing CRBN levels enhanced the ubiquitination and proteasomal degradation of Cav1.2α and decreased I  CaL. In contrast, genetic or pharmacological depletion of CRBN via TD-165, a novel PROTAC-based CRBN degrader, increased surface expression of Cav1.2α and enhanced I  CaL. Low CRBN levels protected the heart against cardiomyopathy in vivo.

Conclusion

Cereblon selectively degrades Cav1.2α, which in turn facilitates cardiac dysfunction. A targeted approach or an efficient method of reducing CRBN levels could serve as a promising strategy for HFrEF therapeutics.
Exposure to lysed bacteria can promote or inhibit growth of neighboring live bacteria depending on local abiotic conditions
Authors: Smakman Fokko , Hall Alex R
Published: February 2022

Microbial death is extremely common in nature, yet the ecological role of dead bacteria is unclear. Dead cells are assumed to provide nutrients to surrounding microbes, but may also affect them in other ways. We found that adding lysate prepared from dead bacteria to cultures of Escherichia coli in nutrient-rich conditions suppressed their final population density. This is in stark contrast with the notion that the primary role of dead cells is nutritional, although we also observed this type of effect when we added dead bacteria to cultures that were not supplied with other nutrients. We only observed the growth-suppressive effect of our dead-bacteria treatment after they had undergone significant lysis, suggesting a key role for cellular contents released during lysis. Transcriptomic analysis indicated changes in gene expression in response to dead cells in growing populations, particularly in genes involved in motility. This was supported by experiments with genetic knockouts and copy-number manipulation. Because lysis is commonplace in natural and clinical settings, the growth-suppressive effect of dead cells we describe here may be a widespread and previously unrecognized constraint on bacterial population growth.
Transcription regulation of iron carrier transport genes by ECF sigma factors through signaling from the cell surface into the cytoplasm
Authors: Braun Volkmar , Hartmann Marcus D , Hantke Klaus
Published: February 2022

Bacteria are usually iron-deficient because the Fe3+ in their environment is insoluble or is incorporated into proteins. To overcome their natural iron limitation, bacteria have developed sophisticated iron transport and regulation systems. In gram-negative bacteria, these include iron carriers, such as citrate, siderophores, and heme, which when loaded with Fe3+ adsorb with high specificity and affinity to outer membrane proteins. Binding of the iron carriers to the cell surface elicits a signal that initiates transcription of iron carrier transport and synthesis genes, referred to as “cell surface signaling”. Transcriptional regulation is not coupled to transport. Outer membrane proteins with signaling functions contain an additional N-terminal domain that in the periplasm makes contact with an anti-sigma factor regulatory protein that extends from the outer membrane into the cytoplasm. Binding of the iron carriers to the outer membrane receptors elicits proteolysis of the anti-sigma factor by two different proteases, Prc in the periplasm, and RseP in the cytoplasmic membrane, inactivates the anti-sigma function or results in the generation of an N-terminal peptide of ∼50 residues with pro-sigma activity yielding an active extracytoplasmic function (ECF) sigma factor. Signal recognition and signal transmission into the cytoplasm is discussed herein.