bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of the Best Option of Brownfield Revitalization Using the Habu Method
Authors: Pelčák Svatopluk , Korytárová Jana 
Published: December 2020

Abstract
The article focuses on the research into the evaluation of the socio-economic efficiency of selected brownfield revitalization projects. Revitalization of brownfields has become the focus of urban planning in recent decades not only in the Czech Republic. The city of Brno has also been involved in the development of these areas for a long time, and the proposal for a new zoning plan, which is currently under discussion, should significantly facilitate the development of such areas. Spatial planning documentation aims at determining the urban concept, the concept of landscape layout and the concept of public infrastructure, it defines the built-up areas, other areas, and corridors and sets the conditions for their use. Regarding the fact that a significant part of these development areas is located in strategically important parts of the city, their use is crucial for their further development. It is therefore appropriate to consider what land-use alternatives are allowed by the zoning plan and how these alternatives can contribute to the effective use of the area in the context of its surroundings and in connection with strategic urban development plans. The main goal of the research is to define a procedure for evaluating individual alternatives of the use of a given area in order to find an optimal solution for both the investor and the city (public). To reach this goal, the HABU method was chosen, which evaluates the development of the area from the point of view of being legally accessible, physically possible, financially feasible and maximally productive, further supplemented by specific elements of cost-benefit analysis (CBA) so as to evaluate the impact of revitalization projects on the broader public space. The output of the research described in this article is a methodical procedure for the evaluation of alternative solutions for the development of brownfields.
A Review on Structural Behavior, Analysis and Design of RC Dapped End Beams
Authors: Shakir Qasim M. 
Published: December 2020

Abstract
This paper represents a historical review of the theoretical and experimental studies carried out previously to study the behavior of reinforced concrete dapped end beams. Prestressing is one of the techniques that have been adopted to enhance the performance of such members. Furthermore, a dapped end needs to be strengthened due to various reasons to improve its performance. Consequently, the review has been extended to include studied such aspects. It was concluded that the ultimate capacity enhanced by reducing the shear-slenderness ratio and horizontal tension reaction and increasing the strength of concrete and fiber content. In addition, nib main reinforcement affects significantly the mode of failure, cracking and ultimate load. However, it was observed that the inclined hanger stirrups or bent performed better than that of vertical alignment and that the prestressing level and strand profile affect the shear capacity and performance significantly. On the other hand, it was found that the external bonding CFRP is the most adopted strengthening material and that the STM (Strut-and-Tie Model) approach results in better predictions of the ultimate load than the shear-friction method. Moreover, directions for future work are proposed, several conclusions have been drawn and a comprehensive list of references is provided.
New Efficient Algorithm for the Discrete Hartley Transform
Authors: Hamood Mounir T. 
Published: December 2020

AbstractIn real-time signal processing applications, the discrete version of the transform introduced by Hartley (DHT) has been proved to be an efficient substitute to the discrete Fourier transform (DFT). A new algorithm for fast calculations of the DHT (FHT) based on radix -2/4/8 method is introduced in this paper. In comparison with the split radix FHT algorithm, the proposed algorithm has a comparable arithmetic complexity, but preserves the regularity and the simple butterfly structure of the radix-2 algorithm. The development of the algorithm is motivated by firstly deriving a new radix-2/8 FHT algorithm and then cascading it with the radix-4 and radix-2 FHT algorithms. The arithmetic complexity of the developed algorithm has been implemented and analyzed by calculating the number of real additions and multiplications for different transform lengths. Comparisons with the existing FHT algorithms have shown that this algorithm can be considered as a good compromise between structural and arithmetic complexity.
The Influence of Various Factors on the Drying Shrinkage of Basalt Fibre Reinforced Cement-Based Composites Designed by the Taguchi Method
Authors: Adesina Adeyemi , Booya Emad , Karla Gorospe , Das Sreekanta 
Published: December 2020

Abstract
Cement-based composites are widely used for various construction applications due to their outstanding mechanical and durability performance. However, the high drying shrinkage of cement-based composites has resulted in detrimental effects on its long-term performance. Drying shrinkage in cement-based composites causes cracks that serve as a pathway for the ingression of deleterious materials into the composites. Therefore, improving the drying shrinkage resistance of cement-based composites will result in an enhancement of the overall performance of the composites. The incorporation of short fibres and supplementary cementitious materials are some of the effective ways to improve the resistance of cement-based composites against drying shrinkage. Therefore, this study aims to evaluate the effect of the incorporation of basalt fibres and fly ash on the drying shrinkage of cement-based composites. This paper presents the results from the experimental and numerical investigation on the influence of various factors on the drying shrinkage of basalt fibre reinforced cement-based composites. The mixtures evaluated in this study were designed using the Taguchi method and a total of nine mixtures were made. The influence of the fly ash, water, sand and basalt content on the drying shrinkage of the mixtures were investigated. The findings from this study showed that the use of fly ash to cement ratio of 4, sand to binder ratio of 1, water to binder ratio of 0.25 and basalt fibre dosage of 2% is optimum to reduce drying shrinkage.
Effect of Radiation on Natural Convection Heat Transfer from Heated Horizontal Cylinder in Vented Enclosure
Authors: Ali Omar Mohammed , Mahmood Raid Ahmed 
Published: December 2020

Abstract
The natural convection heat transfer from a heated circular cylinder placed in a square vented enclosure was investigated considering the effect of the thermal radiation from cylinder using finite volume method with simple algorithm that used pressure-velocity coupling to solve Navier-Stockes and energy equations using Computational Fluid Dynamics CFD (Fluent software). The flow domain is filled with air. The enclosure width is 12.5 cm, two symmetrical openings at its lower and upper walls with size O = 2.5 cm and the cylinder diameter is 5 cm. Different rang of cylinder’s surface emissivity with Rayleigh number range between 103 to 106 was applied in this study as operating condition. The effect of the Ra, cylinder radiation for vented square enclosure on the convection, radiation and total Nusselt numbers Nu and flow and thermal patterns were investigated. The numerical results for pure natural convection were compared with available experimental results, good agreement was obtained. The results revealed that the natural convection heat transfer from the cylinder in the enclosure is increased as compared with that of the unbounded cylinder without radiation effect. The results also revealed that there is a linear relationship between the heat transfer enhancement and the emissivity, there is a significant effect of the cylinder surface radiation which gives high augmentation compared with that of the free cylinder and natural convection heat transfer without radiation effect. A maximum total Nusselt number is obtained at high emissivity compared with that of natural convection heat transfer, the maximum Nu enhancement ranged between 70 to 350 % for low Ra and 25 to 125% for high Ra.
CFD Analysis for The Effect of Personal Ventilation Combined with Mixing Ventilation on Performance Index (ADPI) and Thermal Human Comfort
Authors: Sahebl Hussien Aziz , Mahdi Ala’a Abbas , Al-amir Qusay Rasheed 
Published: December 2020

Abstract
Good indoor air quality and ideal thermal comfort are very important indicators for the comfort of occupant’s space. The Iraqi climate is hot dry in summer, so the use of air conditioners is indispensable. This work focuses on solving the IAQ problems in office room environments, and it evaluated a new principle of ventilation which is combined personal and mixing ventilation systems. Personal and mixing ventilation system can provide individual control of indoor climate. The airflow motion and distribution of temperature investigated numerically with the best flow rate from combined system. CFD study is used for simulation the indoor airflow and temperature distribution by using (AIRPAK3.0.16) for solving the turbulence equations, Naiver-Stocks, energy equations, and using (FVM). The Renormalization Group RNG K-Ɛ turbulence model was used for simulation this study cases, the airflow rate from ATD was 5 l/s and 10 l/s. For mixing ventilation supply temperature of 17°C and The temperature of the supplied air from the personal ventilation system ranges from (17 to 23) °C, it was found that if using personal ventilation system at airflow rate of 10 l / s it would improve the quality of the inhaled air present in the breathing zone. The personal and mixing ventilation system provides good human thermal comfort based on the values of effectiveness temperature (Ɛt) and air distribution performance index (ADPI) which give (1.241) and (63.226%) respectively. The increased airflow rate from (ATD) leads to a decrease in the temperature in the breathing zone, this increases the human thermal comfort of the occupants inside the room.
Effect of TiO2 Nanoparticles Addition on Contact Angle of Epoxy Resin
Authors: Nyief Ali. F. , Shabeeb Kadhum. M. , Hassan Ayad. K. 
Published: December 2020

Abstract
The contact angle is very important parameter in improving the self-cleaning property as well as in increasing the wear resistance of engineering surfaces in addition to improving the thermal transfer properties of materials in general. In this study, titanium dioxide nanoparticles were added to the epoxy resin and sprayed on a substrate of the brass tube used in heat exchangers for the purpose of studying its effect on the angle of contact of the substrate where different proportions of the nanomaterial were added to the epoxy resin in (1%, 3%, 5%, and 7%)wt. The results showed that the contact angle increased with increasing the rate of titanium dioxide nanoparticles.
Impact of synergy effect of SDBS and PVP on morphology and performance of electrolytic copper powder
Authors: Ge Jian , Zhu Xiaoyun , Long Jinming , Liu Shunke 
Published: December 2020

Abstract
Copper powder is prepared by electrolysis, and additives Sodium dodecyl benzene sulfonate (SDBS) and polyvinyl pyrrolidone (PVP) are added to the electrolyte. Through the synergy effect of the two additives, the shielding effect between metal atoms is enhanced, and as a consequence the microscopic morphology is changed and it the powder performance is improved. Scanning electron microscopy (SEM), x-ray diffraction (XRD) and Electrochemical Impedance Spectroscopy (EIS) are used to characterize the copper powder. The results show that when the content of SDBS and PVP is 5 g l−1 and 1.5g l−1 respectively, the new type of thin and long dendrite copper powder can be obtained by electrolysis.
Study Designs for Extending Causal Inferences From a Randomized Trial to a Target Population
Authors: Dahabreh Issa J , Haneuse Sebastien J-P A , Robins James M , Robertson Sarah E , Buchanan Ashley L , Stuart Elizabeth A , Hernán Miguel A 
Published: December 2020

AbstractIn this article, we examine study designs for extending (generalizing or transporting) causal inferences from a randomized trial to a target population. Specifically, we consider nested trial designs, where randomized individuals are nested within a sample from the target population, and nonnested trial designs, including composite data-set designs, where observations from a randomized trial are combined with those from a separately obtained sample of nonrandomized individuals from the target population. We show that the counterfactual quantities that can be identified in each study design depend on what is known about the probability of sampling nonrandomized individuals. For each study design, we examine identification of counterfactual outcome means via the g-formula and inverse probability weighting. Last, we explore the implications of the sampling properties underlying the designs for the identification and estimation of the probability of trial participation.
An Update on the Posterior Earlobe/Concha Mastoid Suspension Suture to Correct “Pixie Ear” Following Facelift: Review of 40 Cases
Authors: Kaye Kai O , Casabona Gabriela R , Paprottka Felix J 
Published: December 2020

AbstractBackgroundAuricular displacement (AD) and earlobe distortion, such as “pixie ear,” are commonly seen deformities after rhytidectomies. In 2018, the authors of this article published a prophylactic technique (posterior earlobe rotation flap [PERF] and concha-mastoid suspension suture [CMSS]) to prevent such cosmetic-related complications in primary facelift surgery. Here, the authors review the utilization of this technique to correct such deformities in patients receiving revision facelift surgeries.ObjectivesThe authors sought to demonstrate the usefulness of this technique in reconstructive cases suffering from such aesthetic deformities.MethodsA total 25 secondary and 15 tertiary rhytidectomies were operated between 2015 and 2018. A combination PERF/CMSS technique was performed bilaterally during each revision facelift surgery (n = 80). A retrospective data analysis (preoperatively; 1 year postoperatively) was conducted to detect any deformities.ResultsNo “pixie ear” deformities were seen in any of our patients postoperatively. AD was detected twice and unilateral hypertrophic scarring once. The postoperative photometric analysis showed a natural ptosis grade I/II in all our patients. The total rate of aesthetic-related complications in our patient cohort was 3.75% (AD: 2.5%; hypertrophic scarring: 1.25%).ConclusionsAfter demonstrating the effectiveness of the PERF and CMSS techniques in primary facelifts, the authors reviewed the technique’s effectiveness for restoring earlobe distortion and AD in secondary or tertiary rhytidectomy cases. In addition to its prophylactic utilization, this method also possesses strong reconstructive power to change tension vectors applied on the face (CMSS) and/or to correct pre-existing aesthetic complications, such as “pixie ear” formation (PERF).Level of Evidence: 4
DeepNOG: fast and accurate protein orthologous group assignment
Authors: Feldbauer Roman , Gosch Lukas , Lüftinger Lukas , Hyden Patrick , Flexer Arthur , Rattei Thomas 
Published: December 2020

Abstract

Motivation
Protein orthologous group databases are powerful tools for evolutionary analysis, functional annotation or metabolic pathway modeling across lineages. Sequences are typically assigned to orthologous groups with alignment-based methods, such as profile hidden Markov models, which have become a computational bottleneck.

Results
We present DeepNOG, an extremely fast and accurate, alignment-free orthology assignment method based on deep convolutional networks. We compare DeepNOG against state-of-the-art alignment-based (HMMER, DIAMOND) and alignment-free methods (DeepFam) on two orthology databases (COG, eggNOG 5). DeepNOG can be scaled to large orthology databases like eggNOG, for which it outperforms DeepFam in terms of precision and recall by large margins. While alignment-based methods still provide the most accurate assignments among the investigated methods, computing time of DeepNOG is an order of magnitude lower on CPUs. Optional GPU usage further increases throughput massively. A command-line tool enables rapid adoption by users.

Availabilityand implementation
Source code and packages are freely available at https://github.com/univieCUBE/deepnog. Install the platform-independent Python program with $pip install deepnog.

Supplementary information
Supplementary data are available at Bioinformatics online.
Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power
Authors: Langouche Lennart , Aralar April , Sinha Mridu , Lawrence Shelley M , Fraley Stephanie I , Coleman Todd P 
Published: December 2020

Abstract

Motivation
The need to rapidly screen complex samples for a wide range of nucleic acid targets, like infectious diseases, remains unmet. Digital High-Resolution Melt (dHRM) is an emerging technology with potential to meet this need by accomplishing broad-based, rapid nucleic acid sequence identification. Here, we set out to develop a computational framework for estimating the resolving power of dHRM technology for defined sequence profiling tasks. By deriving noise models from experimentally generated dHRM datasets and applying these to in silico predicted melt curves, we enable the production of synthetic dHRM datasets that faithfully recapitulate real-world variations arising from sample and machine variables. We then use these datasets to identify the most challenging melt curve classification tasks likely to arise for a given application and test the performance of benchmark classifiers.

Results
This toolbox enables the in silico design and testing of broad-based dHRM screening assays and the selection of optimal classifiers. For an example application of screening common human bacterial pathogens, we show that human pathogens having the most similar sequences and melt curves are still reliably identifiable in the presence of experimental noise. Further, we find that ensemble methods outperform whole series classifiers for this task and are in some cases able to resolve melt curves with single-nucleotide resolution.

Availability and implementation
Data and code available on https://github.com/lenlan/dHRM-noise-modeling.

Supplementary information
Supplementary data are available at Bioinformatics online.
The COVID-19 Ontology
Authors: Sargsyan Astghik , Kodamullil Alpha Tom , Baksi Shounak , Darms Johannes , Madan Sumit , Gebel Stephan , Keminer Oliver , Jose Geena Mariya , Balabin Helena , DeLong Lauren Nicole , Kohler Manfred , Jacobs Marc , Hofmann-Apitius Martin 
Published: December 2020

Abstract

Motivation
The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development.

Results
The ontology comprises 2270 classes of concepts and 38 987 axioms (2622 logical axioms and 2434 declaration axioms). It depicts the roles of molecular and cellular entities in virus-host interactions and in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19. The performance of the ontology has been tested on Medline and the COVID-19 corpus provided by the Allen Institute.

Availabilityand implementation
COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https://github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https://bioportal.bioontology.org/ontologies/COVID-19.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimation of the generation interval using pairwise relative transmission probabilities
Authors: Leavitt Sarah V , Jenkins Helen E , Sebastiani Paola , Lee Robyn S , Horsburgh C Robert , Tibbs Andrew M , White Laura F 
Published: December 2020

Summary
The generation interval (the time between infection of primary and secondary cases) and its often used proxy, the serial interval (the time between symptom onset of primary and secondary cases) are critical parameters in understanding infectious disease dynamics. Because it is difficult to determine who infected whom, these important outbreak characteristics are not well understood for many diseases. We present a novel method for estimating transmission intervals using surveillance or outbreak investigation data that, unlike existing methods, does not require a contact tracing data or pathogen whole genome sequence data on all cases. We start with an expectation maximization algorithm and incorporate relative transmission probabilities with noise reduction. We use simulations to show that our method can accurately estimate the generation interval distribution for diseases with different reproductive numbers, generation intervals, and mutation rates. We then apply our method to routinely collected surveillance data from Massachusetts (2010–2016) to estimate the serial interval of tuberculosis in this setting.
Genetic variations in microRNA-binding sites of solute carrier transporter genes as predictors of clinical outcome in colorectal cancer
Authors: Bendova Petra , Pardini Barbara , Susova Simona , Rosendorf Jachym , Levy Miloslav , Skrobanek Pavel , Buchler Tomas , Kral Jan , Liska Vaclav , Vodickova Ludmila , Landi Stefano , Soucek Pavel , Naccarati Alessio , Vodicka Pavel , Vymetalkova Veronika 
Published: December 2020

Abstract
One of the principal mechanisms of chemotherapy resistance in highly frequent solid tumors, such as colorectal cancer (CRC), is the decreased activity of drug transport into tumor cells due to low expression of important membrane proteins, such as solute carrier (SLC) transporters. Sequence complementarity is a major determinant for target gene recognition by microRNAs (miRNAs). Single-nucleotide polymorphisms (SNPs) in target sequences transcribed into messenger RNA may therefore alter miRNA binding to these regions by either creating a new site or destroying an existing one. miRSNPs may explain the modulation of expression levels in association with increased/decreased susceptibility to common diseases as well as in chemoresistance and the consequent inter-individual variability in drug response. In the present study, we investigated whether miRSNPs in SLC transporter genes may modulate CRC susceptibility and patient’s survival. Using an in silico approach for functional predictions, we analyzed 26 miRSNPs in 9 SLC genes in a cohort of 1368 CRC cases and 698 controls from the Czech Republic. After correcting for multiple tests, we found several miRSNPs significantly associated with patient’s survival. SNPs in SLCO3A1, SLC22A2 and SLC22A3 genes were defined as prognostic factors in the classification and regression tree analysis. In contrast, we did not observe any significant association between miRSNPs and CRC risk. To the best of our knowledge, this is the first study investigating miRSNPs potentially affecting miRNA binding to SLC transporter genes and their impact on CRC susceptibility or patient’s prognosis.