bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of duct shape on the heat dissipation performance of ventilated clutch pressure plate
Authors: Cakmak T , Sevilgen G , Kilic M , Pehlivan A K
Published: February 2021

This study presents the effects of duct design on thermo-fluidic characteristics of ventilated clutch pressure plate via validated numerical model. Two different duct designs are considered. Moreover, variation of duct width and airfoil shaped duct designs are investigated. Compared to non-ventilated conventional clutch pressure plate, results show that implementing duct shape enhances the overall cooling performance by up to 154% at idle speed 550 rpm, 137% at 1200 rpm, and 142% at 2000 rpm. Once only the duct shapes are considered, it is found that the variation of inlet and outlet duct width has negligible effect on overall cooling performance. Further, radial airfoil shaped duct design shows the best cooling performance in overall among all duct shapes, and enhances the overall cooling performance by up to 11% at 550 rpm idle speed compared to non-airfoil radial duct design. In addition, implementation of ventilated design results weight reduction up to 25%. Heat transfer enhancement mechanisms clarified in the present study are helpful to motivate further innovative lightweight solutions in order to overcome the challenges related to the recent CO2 regulation for Heavy Duty Vehicles.
An analytical study on fluid flow characteristics for flow within a microchannel of rectangular cross section
Authors: Joshi R , Simlandi S
Published: February 2021

The present work considers fluid flow analysis within a microchannel of rectangular cross section with different exact and approximate analytical techniques. Thus, velocity slip at the solid wall of the channel is considered. The slip flow is transformed to a no-slip flow with some minor modifications by applying an average slip velocity. The flow is represented by the Navier-Stokes equation exposed to slip boundary conditions. The governing equation is solved considering separation of variables method (SOV) as an exact method and, Integral and Variational methods as approximate methods. The Poiseuille number and slip coefficient are also determined for each method. The present prediction agrees well with available literature. To predict accuracy level of all the techniques, the results are presented in a comparative scale along with numerical prediction. It is observed that the accuracy level for the velocity profile obtained in each technique depends on the aspect ratio where as for the prediction of Poiseuille number and slip coefficient, all the technique show less dependency on the aspect ratio.
Lightweight innovative composite dry clutch pressure plate
Authors: Cakmak T , Cagatay Oter Z , Surmen O
Published: February 2021

This study presents an innovative lightweight composite dry clutch pressure plate including aluminum foam structure in its core. Mechanical burst performance via finite element method of five different composite designs, in which the core foam structure is planned to be obtained via powder metallurgy, is considered. Moreover, a literature review of the powder mixture effect on aluminum foaming experimentation is presented. Compared to conventional serial clutch pressure plate, proposed composite concept reduces the overall weight by up to 47%, however increases stress by up to 65%. Concept design does not only reduces the weight but also enhances the heat dissipation thanks to the increase of convective surface. Mechanisms in the present study are helpful to motivate further innovative lightweight solutions in order to overcome the challenges related to the recent CO2 regulation for Heavy Duty Vehicles.
Experimental investigations on high pressure assisted waste mix cooking oil powered biodiesel fuelled CRDI engine and injection parameter studies
Authors: Kiran C H , Ganesh D B , Banapurmath N R , Ganachari Sharanabasava V
Published: February 2021

The worldwide market estimation of biodiesel is extended to outperform in future. The developing conspicuousness of biofuels as an alternative source instead of customary petroleum products is the critical factor to enhance the market development. Expanding use of biodiesel in power age and automotive fuels is likewise extended to enhance market development over the estimate time frame. For single injection strategies adopted on the performance evaluation of CRDI facility operated engine fueled with waste mix cooking oil (WMCO) B20 blend comparing with the neat Diesel Extraction of Biodiesel from WMCO collected from local area through transesterification test rig is satisfactory. Properties of B20 WMCO biodiesel were determined using ASTM standards were comparable to Diesel fuel. Single injection assisted CRDI engine fuel injection at optimized conditions showed improved overall engine performance at 80% and 100% engine loading operation respectively. For Diesel and B20 WMCO biodiesel, IT of 10ObTDC, IP of 900 bar, and with more number of holes showed excellent performance and were selected as optimized parameters. Retarding the IT from 15° to 10°bTDC increases BTE and reduced emission except for NOx and lower ID, CD and PP, HRR are increased respectively. With keeping IT of 10°bTDC and increasing IP from 600 bar to 900 bar led to further improvement in overall engine performance. Finally increasing the injector holes from 5 to 8 result in the enhanced engine performance with both Diesel and Biodiesel respectively.
Experimental Investigation of Nickel Oxide Nanomaterials with n-Pentane Diesel Blends in Compression Ignition Engine
Authors: Navinprasad A T , Prakash R , Yoganandh J , Meenakshipriya B , Ramakrishnan K
Published: February 2021

The non-renewable energy sources are depleting at higher manner because of greater energy demand. Alternative fuel is a replacement for diesel fuel in compressed ignition engines because of its significant environmental benefits. The use of alternative fuel leads to a reduction in Opacity, NOX, HC and CO emissions and the increase in fuel consumption and the increase in brake thermal efficiency on diesel engines without any modification. The addition of nanoparticles in alternative fuel increases the thermal efficiency and decreases the NOX emission. In this research work, the effect of nano-fuel additives Nickel Oxide (NiO2) on the performance and emission characteristics of n-Pentane alternative fuel in a single cylinder, four strokes, water cooled, and compression injection diesel engine is studied. The nano additives are prepared by precipitation method. The results obtained in particle size below 200 nm, the nanoparticles are characterized by using X-Ray Diffraction. The nanoparticles are dispersed with the alternative fuel by using Ultrasonicator and Magnetic stirrer. The results proved that, these additives will be preferred for reducing the particulate matter, carbon monoxide, unburned hydrocarbons and Nitrogen oxides emission. If the additives are added in the alternative fuel at appropriate proportion, it increases the engine combustion and performance characteristics. This nano-additive is used to reduce the fuel consumption and to improve the thermal efficiency during the experiment.
Stress-strain and absorption of lightweight concrete with artificial lightweight aggregate from diatomaceous earth
Authors: Hasan M , Putra R , Saidi T , Jamil M , Husna N , Syukranlillah M
Published: February 2021

Lightweight concrete can be produced by using artificial lightweight aggregate (ALWA). Diatomaceous earth has extremely low density therefore can be used as a raw material to make ALWA. It is important to understand a stress-strain relationship of materials before they can be used as structural members. This paper presents the stress-strain of lightweight concrete with ALWA from diatomaceous earth based on the experimental observation. In addition, the relationship between the absorption of the lightweight concrete and the immersion time is also presented. Two types of ALWA were produced which are the ALWA made of diatomaceous earth only and the ALWA with the addition of 5% sawdust. A polynomial model of the stress-strain curve was proposed for lightweight concrete containing a different type of ALWA. The absorption of lightweight concrete with ALWA containing sawdust was higher than that of diatomaceous earth only.
Walkability level study in Kota Tua area of Meulaboh district
Authors: Juhardi L , Izziah  , Anggraini R
Published: February 2021

The pedestrian pathway is a facility for pedestrians and also as a means of connecting one region to another on the side of the main road. The case study in this research is in the Kota Tua area of Meulaboh National Road and Teuku Umar Street. As an old city this location has historical value so it attracts people to come. At this location there is also a hawker and culinary center so this location will be crowded to visit. This study was conducted to determine the walkability index of the pedestrian pathway to be studied. Based on the results of observations made, the pedestrian lane in this Kota Tua has a lack of facilities and infrastructure that supports comfort for users. This study uses a mixed-method method where field observations will be conducted to assess the conditions of the pedestrian path. Based on observations made, the results of the walkability index on the National Road, Jalan Iskandar Muda, and Jalan Teuku Umar were declared uncomfortable. Whereas the Area Walkability Index value of 45.75 means it is uncomfortable. Based on the above calculation, the pedestrian path is declared uncomfortable to pass. In order for pedestrian lanes to be comfortable when traversed it is necessary to arrange pedestrian lanes so that pedestrian lanes are comfortable to pass. The structuring carried out refers to Minister of Public Works Regulation No. 3 of 2014.
Priority of provincial road maintenance in Kabupaten Aceh Besar based on analytic hierarchy process method
Authors: Risdiawati  , Saleh S M , Isya M
Published: February 2021

Road damage that has occurred on several roads has caused enormous losses, especially for road users, such as long travel times, congestion, accidents, and others. It is necessary to pay attention to this so that there is no deterioration in road quality due to road surface damage so that it can affect safety, comfort, and smoothness of traffic. Therefore, researchers damaged road surface conditions, which can affect the travel time of the vehicle. The purpose of this research is to identify the type and level of road damage and to determine road-handling priorities. The results of calculating the condition of each provincial road section in the Aceh Besar District using the PCI method are included in the very good, good and moderate categories, so that the type of handling can be determined is routine maintenance. From the results of the analysis of respondents by using Analytic Hierarchy Process (AHP), said that the priority road-handling by using several criteria, namely: the order of 1 is the type of treatment with a weight of 0.47, then the second is the condition of the road with a weight of 0.37, then the third-order is accessibility with a weight of 0.12, and the fourth place is a land use with a weight of 0.04. As for the alternative road-handling priority obtained a score’s greatest at road Keutapang Dua - Mata Ie with the acquisition of a score of 0.34, then alternate both at road Batas Kota Banda Aceh - Sp. Lam Ateuk 0.32, the third alternative on road Ir. M. Thaher 0.26, for the fourth alternative on road Sp. Lamreueng-Sp. Cot Iri 0.06, the fifth alternative on road Kota Jantho-Alue Glong 0.011, the sixth alternative on road Bts. Banda Aceh-Blang Bintang 0.010, and for the seventh alternative on road Krueng Raya - Batas Pidie with a score of 0.003. The first priority for road handling based on an assessment of road conditions using the PCI method is road Krueng Raya - Batas Pidie section.
Environmental adaptation and hazard reduction strategies in relocation housing development by its occupants case: Indo-Tiongkok housing, Neuheun Aceh Besar
Authors: Wulandari E , Zahriah  , Fuadi Z
Published: February 2021

The construction of relocation housing is a form of housing assistance for victims of the 2004 tsunami, with various environmental designs. Indo-Tiongkok housing (Jacky Chan housing) is one of the relocation housing in the Neuheun area, designed with an approach adjusting the hilly topography. The disadvantage of building on contoured land is that it is susceptible to local erosion, which can damage buildings on the land (roads and buildings). This study reveals the phenomenon of environmental adaptation strategies by the community to reduce the risk of hazards in their home environment, and this is important to disclose to find out people’s attitudes and actions in maintaining the sustainability of their living space. The research method was in-depth interviews with the community to understand the understanding of environmental hazards and community strategies in reducing the risk of dangers that might occur. The information required relates to 2 things: 1) types of environmental hazards, risks, and patterns of threats; 2) attitudes and strategies of society to overcome these dangers. The results showed that the community understands the risk of hazards logically, by looking at signs of natural elements such as traces of erosion, and the impact on artificial elements (houses, soil, yard boundaries). The community strategy to reduce the risk of hazards is to combine various factors from engineering aspects (building materials and techniques), economic aspects, and suitability aspects of plant selection. Results showed that the strategy for adaptation patterns to the environment would appear in each occupant according to their problems and abilities so that the results of the appearance of the residential environment design would vary. This is so unique in the culture of living in each place, which will distinguish it from other places.
Characterization and utilization of coconut coir and bentonite-based adsorbents for removal of lead metal ion from hazardous liquid waste
Authors: Mariana  , Mulana F , I Perkasa B , T Muhamad A F
Published: February 2021

Adsorbent is one of the most commonly used materials because of its high adsorption effectiveness. However, adsorption with one type of adsorbent causes a lower adsorption efficiency. This study aims to determine the characterization of adsorbents from coconut coir and bentonite-based adsorbents and the combined adsorbent from coconut coir charcoal and bentonite and to examine the adsorption capacity of lead metal ion on these adsorbents. The types of adsorbents used in this study were coconut coir charcoal without activation, coconut coir charcoal with activation, pure bentonite, bentonite with activation, and combination of activated coconut coir charcoal: activated bentonite with mass ratio of 70:30. The research was initiated with pyrolysis of coconut coir at temperature of 400°C, then activated chemically with 0.3 M HCl solution. The resulting adsorbents were characterized using Scanning Electron Microscopy (SEM) to determine the morphological structure, Fourier Transform Infra-Red Spectrophotometer (FTIR) to determine the functional groups, X-Ray Diffraction (XRD) to determine the crystalline structure. Then the adsorption of lead metal ions was carried out by using these adsorbents. The results showed that the best adsorption efficiency is by adsorbent combination of activated coconut coir charcoal: activated bentonite with mass ratio of 70:30. The adsorption efficiency of lead metal ions using activated coir adsorbents: activated bentonite (70:30) is 35.0%. The activated coconut coir charcoal: activated bentonite with mass ratio of 70:30 has the largest adsorption capacity of lead metal ions which is 182.71 mg/gr.
Characterization of polyethersulfone (PES) membrane entrapping with ginger extract (GE) as a green additive
Authors: Fahrina A , Arahman N , Mulyati S , Aprilia S , Bilad M R
Published: February 2021

The hydrophilicity of the membrane surface plays an essential role in improving membrane filtration performance. Better hydrophilicity could facilitate higher water permeation and prevent fouling phenomena. In this research, a green additive from ginger extract (GE) was employed to improve the polyethersulfone (PES) membrane hydrophilicity. The PES/GE membrane was fabricated via the phase inversion method by dispersing GE powder in PES/NMP solution using sonication followed by mechanical stirred. The influence of ginger extract (GE) on the PES membrane was characterized in terms of hydrophilicity, morphological structure, porosity, water permeation, chemical composition, and mechanical property. Water contact angle measurements showed that PES/GE membrane with 0.1% GE has the highest hydrophilicity. Scanning Electron Microscopy (SEM) indicated a porous finger-like structure on the cross-section membrane after the addition of GE.
Molecular docking study of fatty acids from Pliek U Oil in the inhibition of SARS-CoV-2 protein and enzymes
Authors: Khairan K , Idroes R , Tumilaar S G , Tallei T E , Idroes G M , Rahmadhany F , Futri M U , Dinura N M , Mauliza S , Diana M , Maisarah C P , Maulana A , Noviandy T R , Suhendra R , Muslem  , Earlia N
Published: February 2021

This study aimed to analyze the fatty acidinPliek Uoil andevaluate its inhibitor potential based on the interaction to several proteins and enzymes in SARS-CoV-2 using the in silico approach.Pliek Uoil containing capric acid, caprylic acid, lauric acid, linoleic acid, myristic acid, oleic acid, and palmitic acids, with oleic acid as a dominant substance. Molecular docking analysis showed that linoleic acid has the best interaction to the receptors with the lowest binding affinity to 3CLpro (6LU7), Spike protein (6VXX), PLpro (6WX4), RdRp (6M71), E protein (5X29), and Spike Ectodomain Structure (6VYB) of -4.9, -5.8, -4.7, -4.3, -5.3 and -5.5 kcal/mol, respectively. The finding suggests that the binding of linoleic acid to the SARS-CoV-2 protein and enzyme may cause impairment of viral attachments to host cells, thus reducing infectivity in COVID-19 patients.
Identification of Gayo arabic coffee beans and powder using the FTIR-PCA combination method
Authors: Akbar Z , Idroes R , Ginting B , Karma T , Rahimah S , Helwani Z , Yusuf M
Published: February 2021

The identification of Gayo Arabica coffee beans and coffee powder has been done to classify coffee plantation from several different regions using FTIR Spectroscopy and Principal Component Analysis (PCA). Samples were taken by purposive sampling from the Arabica coffee plantations in Pegasing, Jagong, and Celala areas, Aceh Tengah Regency, and also in Bandar, Permata, and Wih Pesam areas, Bener Meriah Regency. FTIR analyzed both the dry Gayo Arabica coffee beans and powder in the wavelength range of 4000 cm−1-400 cm−1. The spectra resulted were analyzed using PCA. FTIR spectra show the absorption of typical functional groups of caffeine, namely O-H (3400 cm−1), C-H aromatic (2900 cm−1), C-H aliphatic (2800 cm−1), C=O (1743 cm−1), C=C ( 1640 cm−1), C=C aromatic (1550 cm−1), C-H alkanes (1450 cm−1) and C-N (1240 cm−1). There was a loss of absorption of C=O and C-N groups in coffee powder samples from the Pegasing, Jagong, and Permata areas caused by high-temperature heating during the coffee powder making process. The PCA showed that coffee bean samples could be distinguished properly based on the coffee origin location, namely Aceh Tengah and Bener Meriah Regencies. Meanwhile, coffee powder samples showed poor separation of PCA plot patterns between coffee powder from the two regions. It can be concluded that the PCA method can be used for the classification of both Gayo Arabica coffee beans and powder, where the classification of beans is better than powder.
Joint relay selection and energy harvesting to improve performance of cooperative communication systems
Authors: Berutu E , Muharar R , Nasaruddin N
Published: February 2021

This paper focuses on a combining relay selection with energy harvesting (EH), known as joint relay selection with EH (JRSEH), to improve performance in wireless cooperative communication systems. Previous research was examined performance improvement with relay selection (RS) techniques without combined with EH (RS non-EH). This study aims to improve the performance by applying EH and the RS in the cooperative communication system. In the system, a source selects the best relay from several relays that produce the highest SNR value at the destination. The selected best relay performs EH based on time switching. Then, the best relay with EH obtains the power to forward information to the destination using the Amplify and Forward (AF) relay scheme. The channel from source to relay is Rician fading, and from the relay to a destination is Rayleigh fading. The research method used is system modeling and analysis of computer simulations. The system performance is calculated based on the bit error rate (BER) and the throughput in a multi-relay cooperative system with EH and RS. The results show that the performance of the proposed JRSEH higher than that of RS non-EH, multi-relay EH, and multi-relay non-EH.
Performance analysis of mAlexnet by training option and activation function tuning on parking images
Authors: Rahman S , Ramli M , Arnia F , Muharar R , Sembiring A
Published: February 2021

Information on the availability of parking spaces is one of the main needs in urban areas. This information can minimize the impact of vehicle growth, including exhaust gas emissions, traffic jams, and fuel use. In general, the detection of parking space availability can be done in two ways, namely the sensor system and computer vision. Computer vision monitoring of parking spaces is more promising for use in the future. A single-camera can monitor multiple parking spaces by making use of computer vision. CNN is a technique for parking space classification. CNN’s pre-trained dedicated to parking space classification is mAlexnet. mAlexnet can classify parking spaces well, but not perfect. in this paper, we try to observe and improve the performance of mAlexnet. We tried training options and activation function tuning. From the results of testing the combination of SGDM training option and the LeakyReLu activation function, the performance of mAlexnet improves.
Uniform stability and uniform-in-time mean-field limit of the thermodynamic Kuramoto model
Authors: Ha Seung-Yeal , Kang Myeongju , Park Hansol , Ruggeri Tommaso , Shim Woojoo
Published: February 2021

We consider the thermodynamic Kuramoto model proposed in \cite{H-P-R-S}. For each oscillator in thermodynamic Kuramoto model, there is a coupling effect between the phase and the temperature field. For such a model, we study a uniform stability and uniform-in-time mean-field limit to the corresponding kinetic equation. For this, we first derive a uniform

ℓ
p

\ell ^p

-stability of the thermodynamic Kuramoto model with respect to initial data by directly estimating the temporal evolution of

ℓ
p

\ell ^p

-distance between two admissible solutions to the particle thermodynamic Kuramoto model. In a large-oscillator limit, the Vlasov type mean-field equation can be rigorously derived using the BBGKY hierarchy, uniform stability estimate, and particle-in-cell method. We construct unique global-in-time measure-valued solutions to the derived kinetic equation and also derive a uniform-in-time stability estimate and emergent estimates.
Hate Crimes in a Cross-Cultural Context
Authors: Sheppard Keller G. , Lawshe Nathaniel L. , McDevitt Jack
Published: February 2021

Hate crimes are criminal offenses that involve elements of bias based on some individual characteristics of the victim, including race, gender, disability, sexual orientation, and religion. The passage of laws criminalizing or enhancing the punishment for crimes featuring bias motivations has been met with intense controversy. In addressing criticism of such legislation, proponents of these laws highlight the considerable harms caused by hate crime. These incidents are considered especially heinous as they not only violate the civil and human rights of the immediate victim but also send a message of fear to the entirety of that victim’s community or social group. Prior scholarship on these offenses have employed numerous theoretical frameworks—psychological, historical, sociological, and economic theories—to describe why perpetrators target victims based on perceived group identity. Other work has provided insight into the causes of hate crime by considering factors distinguishing bias-motivated offenders from other criminal offenders. Conflicting legal definitions of hate crime add to the complexity of its conceptualization. At the international level, hate crime statutes are strongly influenced by the different social, cultural, and historical contexts across nations. Hate crime laws differ markedly across countries with respect to the specification of protected groups’ identities, treatment of hate speech, legal standards for establishing bias motivation, and utilization of hate crime statutes for criminal prosecutions. These differences, coupled with nationally distinct methodologies for recording bias-motivated incidents, have stymied attempts to engage in cross-national comparisons of the quality and extent of hate crime.
Tradition and Transformation in Danish Early Childhood Education and Care
Authors: Dannesboe Karen Ida , Kjær Bjørg
Published: February 2021

Denmark has a long tradition of public provision of early childhood education and care (ECEC) as part of what is known internationally as the Nordic welfare model. Both traditions and transformations within Danish ECEC are parallel to the establishment and development of this model. The emergence of child-centered pedagogy, so characteristic for Danish ECEC, is part of specific historical processes. Since the 1960s, the ECEC sector has undergone significant expansion and in 2020, most children in Denmark between the ages of 1 and 6 attend an ECEC institution. This expansion has positioned ECEC as a core universal welfare service, including a special focus on preventing injustice and inequality and on taking care of the vulnerable and disadvantaged. Early 21st-century international discourses on learning and early intervention have influenced political reforms and initiatives addressing ECEC institutions and the work of “pedagogues” (the Danish term for ECEC practitioners with a bachelor’s degree in social pedagogy). Since the 1990s, there has been growing political interest in regulating the content of ECEC, resulting in various policies and reforms that have changed the nature of Danish ECEC by introducing new learning agendas. This has been accompanied by an increased focus on the importance of the early years of childhood for outcomes later in life and on the role of parents in this regard. These tendencies are embedded in political initiatives and discourses and shape the conditions for ECEC, perceptions of children and childhood, the legitimacy of the pedagogical profession, the meaning of and emphasis on young children’s learning, the importance of inclusion, and the changing role of parents. These changes in social reforms and pedagogical initiatives interact with national historical processes and international tendencies and agendas at different levels.
Root hairs are the most important root trait for rhizosheath formation of barley (Hordeum vulgare), maize (Zea mays) and Lotus japonicus (Gifu)
Authors: Burak Emma , Quinton John N , Dodd Ian C
Published: February 2021

Background and Aims

Rhizosheaths are defined as the soil adhering to the root system after it is extracted from the ground. Root hairs and mucilage (root exudates) are key root traits involved in rhizosheath formation, but to better understand the mechanisms involved their relative contributions should be distinguished.

Methods

The ability of three species [barley (Hordeum vulgare), maize (Zea mays) and Lotus japonicus (Gifu)] to form a rhizosheath in a sandy loam soil was compared with that of their root-hairless mutants [bald root barley (brb), maize root hairless 3 (rth3) and root hairless 1 (Ljrhl1)]. Root hair traits (length and density) of wild-type (WT) barley and maize were compared along with exudate adhesiveness of both barley and maize genotypes. Furthermore, root hair traits and exudate adhesiveness from different root types (axile versus lateral) were compared within the cereal species.

Key Results

Per unit root length, rhizosheath size diminished in the order of barley > L. japonicus > maize in WT plants. Root hairs significantly increased rhizosheath formation of all species (3.9-, 3.2- and 1.8-fold for barley, L. japonicus and maize, respectively) but there was no consistent genotypic effect on exudate adhesiveness in the cereals. While brb exudates were more and rth3 exudates were less adhesive than their respective WTs, maize rth3 bound more soil than barley brb. Although both maize genotypes produced significantly more adhesive exudate than the barley genotypes, root hair development of WT barley was more extensive than that of WT maize. Thus, the greater density of longer root hairs in WT barley bound more soil than WT maize. Root type did not seem to affect rhizosheath formation, unless these types differed in root length.

Conclusions

When root hairs were present, greater root hair development better facilitated rhizosheath formation than root exudate adhesiveness. However, when root hairs were absent root exudate adhesiveness was a more dominant trait.
Gene expression underlying floral epidermal specialization in Aristolochia fimbriata (Aristolochiaceae)
Authors: Suárez-Baron Harold , Alzate Juan F , González Favio , Pelaz Soraya , Ambrose Barbara A , Pabón-Mora Natalia
Published: February 2021

Background and Aims

The epidermis constitutes the outermost tissue of the plant body. Although it plays major structural, physiological and ecological roles in embryophytes, the molecular mechanisms controlling epidermal cell fate, differentiation and trichome development have been scarcely studied across angiosperms, and remain almost unexplored in floral organs.

Methods

In this study, we assess the spatio-temporal expression patterns of GL2, GL3, TTG1, TRY, MYB5, MYB6, HDG2, MYB106-like, WIN1 and RAV1-like homologues in the magnoliid Aristolochia fimbriata (Aristolochiaceae) by using comparative RNA-sequencing and in situ hybridization assays.

Key Results

Genes involved in Aristolochia fimbriata trichome development vary depending on the organ where they are formed. Stem, leaf and pedicel trichomes recruit most of the transcription factors (TFs) described above. Conversely, floral trichomes only use a small subset of genes including AfimGL2, AfimRAV1-like, AfimWIN1, AfimMYB106-like and AfimHDG2. The remaining TFs, AfimTTG1, AfimGL3, AfimTRY, AfimMYB5 and AfimMYB6, are restricted to the abaxial (outer) and the adaxial (inner) pavement epidermal cells.

Conclusions

We re-evaluate the core genetic network shaping trichome fate in flowers of an early-divergent angiosperm lineage and show a morphologically diverse output with a simpler genetic mechanism in place when compared to the models Arabidopsis thaliana and Cucumis sativus. In turn, our results strongly suggest that the canonical trichome gene expression appears to be more conserved in vegetative than in floral tissues across angiosperms.
NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction
Authors: Xiang Ju , Zhang Jiashuai , Zheng Ruiqing , Li Xingyi , Li Min
Published: February 2021

The prediction of genes related to diseases is important to the study of the diseases due to high cost and time consumption of biological experiments. Network propagation is a popular strategy for disease-gene prediction. However, existing methods focus on the stable solution of dynamics while ignoring the useful information hidden in the dynamical process, and it is still a challenge to make use of multiple types of physical/functional relationships between proteins/genes to effectively predict disease-related genes. Therefore, we proposed a framework of network impulsive dynamics on multiplex biological network (NIDM) to predict disease-related genes, along with four variants of NIDM models and four kinds of impulsive dynamical signatures (IDSs). NIDM is to identify disease-related genes by mining the dynamical responses of nodes to impulsive signals being exerted at specific nodes. By a series of experimental evaluations in various types of biological networks, we confirmed the advantage of multiplex network and the important roles of functional associations in disease-gene prediction, demonstrated superior performance of NIDM compared with four types of network-based algorithms and then gave the effective recommendations of NIDM models and IDS signatures. To facilitate the prioritization and analysis of (candidate) genes associated to specific diseases, we developed a user-friendly web server, which provides three kinds of filtering patterns for genes, network visualization, enrichment analysis and a wealth of external links (http://bioinformatics.csu.edu.cn/DGP/NID.jsp). NIDM is a protocol for disease-gene prediction integrating different types of biological networks, which may become a very useful computational tool for the study of disease-related genes.
Developing intuitive and explainable algorithms through inspiration from human physiology and computational biology
Authors: Turki Houcemeddine , Taieb Mohamed Ali Hadj , Aouicha Mohamed Ben
Published: February 2021

In this letter, we explain how intuitive and explainable methods inspired from human physiology and computational biology can serve to simplify and ameliorate the way we process and generate knowledge resources.
An enhanced loss function simplifies the deep learning model for characterizing the 3D organoid models
Authors: Winkelmaier Garrett , Parvin Bahram
Published: February 2021

Motivation

Organization of the organoid models, imaged in 3D with a confocal microscope, is an essential morphometric index to assess responses to stress or therapeutic targets. In fact, differentiating malignant and normal cells is often difficult in monolayer cultures. But in 3D culture, colony organization can provide a clear set of indices for differentiating malignant and normal cells. The limiting factors are delineating each cell in a 3D colony in the presence of perceptual boundaries between adjacent cells and heterogeneity associated with cells being at different cell cycles.

Results

In a previous paper, we defined a potential field for delineating adjacent nuclei, with perceptual boundaries, in 2D histology images by coupling three deep networks. This concept is now extended to 3D and simplified by an enhanced cost function that replaces three deep networks with one. Validation includes four cell lines with diverse mutations, and a comparative analysis with the UNet models of microscopy indicates an improved performance with the F1-score of 0.83.

Availability and implementation

All software and annotated images are available through GitHub and Bioinformatics online. The software includes the proposed method, UNet for microscopy that was extended to 3D and report generation for profiling colony organization.

Supplementary information

Supplementary data are available at Bioinformatics online.
Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography
Authors: Du Xuefeng , Wang Haohan , Zhu Zhenxi , Zeng Xiangrui , Chang Yi-Wei , Zhang Jing , Xing Eric , Xu Min
Published: February 2021

Motivation

Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications in life science. However, the systematic structural recognition and recovery of macromolecules captured by cryo-ET are difficult due to high structural complexity and imaging limits. Deep learning-based subtomogram classification has played critical roles for such tasks. As supervised approaches, however, their performance relies on sufficient and laborious annotation on a large training dataset.

Results

To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labeling from a large unlabeled subtomogram pool. Firstly, HAL adopts uncertainty sampling to select the subtomograms that have the most uncertain predictions. This strategy enforces the model to be aware of the inductive bias during classification and subtomogram selection, which satisfies the discriminativeness principle in AL literature. Moreover, to mitigate the sampling bias caused by such strategy, a discriminator is introduced to judge if a certain subtomogram is labeled or unlabeled and subsequently the model queries the subtomogram that have higher probabilities to be unlabeled. Such query strategy encourages to match the data distribution between the labeled and unlabeled subtomogram samples, which essentially encodes the representativeness criterion into the subtomogram selection process. Additionally, HAL introduces a subset sampling strategy to improve the diversity of the query set, so that the information overlap is decreased between the queried batches and the algorithmic efficiency is improved. Our experiments on subtomogram classification tasks using both simulated and real data demonstrate that we can achieve comparable testing performance (on average only 3% accuracy drop) by using less than 30% of the labeled subtomograms, which shows a very promising result for subtomogram classification task with limited labeling resources.

Availability and implementation

https://github.com/xulabs/aitom.

Supplementary information

Supplementary data are available at Bioinformatics online.
Molecular biogeography of the fungus-dwelling saproxylic beetle Bolitophagus reticulatus indicates rapid expansion from glacial refugia
Authors: Eberle Jonas , Husemann Martin , Doerfler Inken , Ulrich Werner , Müller Jörg , Bouget Christophe , Brin Antoine , Gossner Martin M , Heilmann-Clausen Jacob , Isacsson Gunnar , Krištín Anton , Lachat Thibault , Larrieu Laurent , Rigling Andreas , Schmidl Jürgen , Seibold Sebastian , Vandekerkhove Kris , Habel Jan Christian
Published: February 2021

The geographical distributions of species associated with European temperate broadleaf forests have been significantly influenced by glacial–interglacial cycles. During glacial periods, these species persisted in Mediterranean and extra-Mediterranean refugia and later, during interglacial periods, expanded northwards. The widespread saproxylic beetle Bolitophagus reticulatus depends closely on European temperate broadleaf forests. It usually develops in the tinder fungus Fomes fomentarius, a major decomposer of broadleaf-wood. We sampled B. reticulatus in sporocarps from European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis) across Europe and the Caucasus region. We analysed mitochondrial gene sequences (cox1, cox2, cob) and 17 microsatellites to reconstruct the geographical distribution of glacial refugia and postglacial recolonization pathways. We found only marginal genetic differentiation of B. reticulatus, except for a significant split between populations of the Caucasus region and Europe. This indicates the existence of past refugia south of the Great Caucasus, and a contact zone with European populations in the Crimean region. Further potential refugia might have been located at the foothills of the Pyrenees and in the Balkan region. Our genetic data suggest a phalanx-wise recolonization of Europe, a reflection of the high mobility of B. reticulatus.
Incarceration as a Fundamental Social Cause of Health Inequalities: Jails, Prisons and Vulnerability to COVID-19
Authors: Novisky Meghan A , Nowotny Kathryn M , Jackson Dylan B , Testa Alexander , Vaughn Michael G
Published: February 2021

Although research has established the disproportionate health burdens among incarcerated persons, the literature has yet to identify a theoretical framework for outlining the harms of incarceration associated with pandemics. We advance the literature theoretically by arguing two points. First, we assert that incarceration is a potent structural driver of health inequalities that must be considered as a fundamental social cause of disease. To underscore this point, we review how incarceration meets each of the four fundamental social cause criteria originally proposed by Link and Phelan. Second, given that incarceration is a fundamental social cause of disease, both currently and formerly incarcerated populations are likely to face heightened vulnerabilities to pandemics, including COVID-19, further exacerbating health disparities among incarceration-exposed groups.
Place, Strengths and Assets: A Case Study of How Local Area Coordination is Supporting Individuals and Families Under Conditions of Austerity
Authors: Bainbridge Laura , Lunt Neil
Published: February 2021

We report findings of a mixed-method evaluation of Local Area Coordination (LAC) in one English Local Authority—an approach that draws on principles of earlier intervention, and place-, asset- and strengths-based activity. We drew on documentary materials, unstructured observation and qualitative interviews. In total, fifty-five qualitative interviews were conducted with professional stakeholders (including Coordinators, statutory agencies and community organisations), and a purposive sample of individuals supported by LAC. Positively, LAC is operating as intended. It is a flexible and agile approach, and one that is less constrained by the expectations and methods associated with traditional service delivery. Reported impacts include: tackling isolation and loneliness; building a positive vision of the future; identifying non-service solutions and being heard. We discuss the ongoing conceptual and methodological challenges to building the LAC evidence base, fostering professional support and understanding, and managing expectations of individuals and communities in furthering development. Resolving these would allow LAC to move beyond being a promising, local and small-scale transformative development for individuals and families. Its future trajectory is enmeshed in the implications of COVID-19 for individuals, families and communities: rising poverty and widening inequality, a fragile Third Sector, and concerns about community fatigue and erosion of trust.
Age-Related Differences in White Matter: Understanding Tensor-Based Results Using Fixel-Based Analysis
Authors: Kelley Shannon , Plass John , Bender Andrew R , Polk Thad A
Published: February 2021

Aging is associated with widespread alterations in cerebral white matter (WM). Most prior studies of age differences in WM have used diffusion tensor imaging (DTI), but typical DTI metrics (e.g., fractional anisotropy; FA) can reflect multiple neurobiological features, making interpretation challenging. Here, we used fixel-based analysis (FBA) to investigate age-related WM differences observed using DTI in a sample of 45 older and 25 younger healthy adults. Age-related FA differences were widespread but were strongly associated with differences in multi-fiber complexity (CX), suggesting that they reflected differences in crossing fibers in addition to structural differences in individual fiber segments. FBA also revealed a frontolimbic locus of age-related effects and provided insights into distinct microstructural changes underlying them. Specifically, age differences in fiber density were prominent in fornix, bilateral anterior internal capsule, forceps minor, body of the corpus callosum, and corticospinal tract, while age differences in fiber cross section were largest in cingulum bundle and forceps minor. These results provide novel insights into specific structural differences underlying major WM differences associated with aging.
Development and Validation of an Administrative Codes Algorithm to Identify Abdominal Surgery and Bowel Obstruction in Patients With Inflammatory Bowel Disease
Authors: Gandle Cassandra , Scott Frank I , Waljee Akbar , Vajravelu Ravy K , Sansgiry Shubhada , Hou Jason K
Published: February 2021

Background

Validated administrative codes (CPT and ICD) can permit the use of large databases to study diseases and outcomes. The aim of this study was to validate administrative codes for surgery and obstructive complications in patients with inflammatory bowel disease (IBD).

Methods

We performed a retrospective study of IBD patients within the Veterans Affairs Health Administration (VA) from 2000 to 2015 with administrative codes for bowel surgery and complications validated by chart review. Positive predictive values (PPVs) and negative predictive value (NPV) were calculated.

Results

The PPV for bowel surgery was 96.4%; PPV of obstruction codes for bowel obstruction was 80.5% (95% confidence interval: 69.1%, 89.2%).

Conclusions

CPT and ICD codes for abdominal surgery and obstructive complications can be accurately utilized in IBD patients in VA.
Incidental finding and conservative management of left main coronary atresia in an adult patient: a case report
Authors: Talanas Giuseppe , Corda Giulia , Parodi Guido , Portoghese Michele
Published: February 2021

Background

Left main (LM) coronary atresia (LMCA) is a rare coronary anomaly where the LM is congenitally absent and a variable clinical spectrum can follow. The diagnosis of LMCA is generally made in youth because of the development of symptoms, but very rarely in adulthood. In symptomatic patients, surgical revascularization is recommended, whereas, in asymptomatic patients with LMCA and without inducible myocardial ischaemia, preventive surgical treatment is controversial.

Case summary

A 58-year-old male patient with aortic ectasia detected during an echocardiogram performed to evaluate a hypertension-related preclinical cardiac damage and, due to this finding, an echocardiographic follow-up was suggested. Three years later, he was admitted to undergo coronary angiography (CA) after the computed tomography finding of a suspected occlusion of the LM with collateral circulation from right coronary artery (RCA) to left anterior descending and circumflex arteries. CA confirmed an LMCA and the RCA provided blood supply to the left coronary artery through collaterals whose calibre was similar to that of the target left-sided vessels. No obstructive coronary artery disease was detected. In order to detect potential myocardial ischaemia, a technetium-tetrofosmin cardiac single-photon emission computed tomography during maximal exercise-stress test was performed and it did not show a perfusion defect. Medical management with scheduled follow-up visits was deemed to be the best therapeutic option.

Discussion

LMCA is a rare anomaly where LM is absent and the RCA provides collateral circulation for left coronary artery. In asymptomatic patients, preventive surgical treatment is controversial.