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Papers are the most commonly used substrates. A printable paper must have certain properties. These properties include surface smoothness, air permeability, surface energy, colour of the paper, opacity, whiteness, light fastness, gloss, and coefficient of elongation under force. In addition, a good printable paper should not allow ink to pass between its two surfaces. After the papers are produced, they are subjected to surface treatments in order to improve the above-mentioned properties and to provide extra specification. Surface treatments include calendering, surface sizing and coating processes. While filling the recesses and protrusions on the surface with the coating process, the paper's affinity for the ink is increased, and the penetration of the ink to the other surface of the paper is prevented. In the coating process basically, a filler is dispersed in a binder. In this study, it is aimed to obtain the highest quality and most printable paper by changing the type of binder used in the coating. In this study, equal amount (5% w/w) titanium dioxide filler was used in all coating formulations. In coating formulations; cationic starch, hydroxy ethyl cellulose and polyvinyl alcohol polymers were used as binders. Binder amounts are adjusted according to optimum viscosity. The obtained coating formulations were coated on the paper surface with a laboratory type coating device. Colour, gloss, surface smoothness, air permeability, surface energy and surface morphology of the coated papers were determined. It was printed with magenta offset printing ink on three different types of paper coated with different binders, using the IGT C1 offset printability test device, under 400 N/m2 pressure printing conditions. Colour and gloss measurements of the prints were made. As a result; It was determined that three different binders improved the printability parameters.

One way of exposing predatory journals is to submit a spoof article to see if it gets accepted. We investigate one journal, looking at how it has performed since a spoof paper it accepted came to light. We find that it has published almost 20% more papers following the acceptance of the spoof paper. The journal has a new web site, which appears to show that it did not publish its first paper until 2018. However, there is an old web site that lists 321 papers dating back to 2012. The editors said that this is due to a new workflow system, which meant that previously published papers could not be listed on the new web site. Moreover, the number of papers could be not accommodated, as a high configuration server would be required to provide a responsive web site. We found some plagiarism, which looks quite serious. We conclude that the spoof paper had little effect on the journal, which continues to operate, seven years after the spoof paper was accepted.

We consider the problem of communicating over a channel that randomly “tears” the message block into small pieces of different sizes and shuffles them. For the binary torn-paper channel with block length $n$ and pieces of length ${\mathrm{ Geometric}}(p_{n})$ , we characterize the capacity as $C = e^{-\alpha }$ , where $\alpha = \lim _{n\to \infty } p_{n} \log n$ . Our results show that the case of ${\mathrm{ Geometric}}(p_{n})$ -length fragments and the case of deterministic length- $(1/p_{n})$ fragments are qualitatively different and, surprisingly, the capacity of the former is larger. Intuitively, this is due to the fact that, in the random fragments case, large fragments are sometimes observed, which boosts the capacity.

In this work, some counterexamples are given to refute some results in the paper by Kohli [RAIRO:OR 53 (2019) 1617–1632]. We correct the fault in some of his results.

Formulaic expressions, such as 'in this paper we propose', are helpful for authors of scholarly papers because they convey communicative functions; in the above, it is showing the aim of this paper'. Thus, resources of formulaic expressions, such as a dictionary, that could be looked up easily would be useful. However, forms of formulaic expressions can often vary to a great extent. For example, 'in this paper we propose', 'in this study we propose' and 'in this paper we propose a new method to' are all regarded as formulaic expressions. Such a diversity of spans and forms causes problems in both extraction and evaluation of formulaic expressions. In this paper, we propose a new approach that is robust to variation of spans and forms of formulaic expressions. Our approach regards a sentence as consisting of a formulaic part and non-formulaic part. Then, instead of trying to extract formulaic expressions from a whole corpus, by extracting them from each sentence, different forms can be dealt with at once. Based on this formulation, to avoid the diversity problem, we propose evaluating extraction methods by how much they convey specific communicative functions rather than by comparing extracted expressions to an existing lexicon. We also propose a new extraction method that utilises named entities and dependency structures to remove the non-formulaic part from a sentence. Experimental results show that the proposed extraction method achieved the best performance compared to other existing methods., 21 pages, 11 figures

In over fve years, Bornmann, Stefaner, de Moya Anegon, and Mutz (2014b) and Bornmann, Stefaner, de Moya Anegón, and Mutz (2014c, 2015) have published several releases of the www.excellencemapping.net tool revealing (clusters of) excellent institutions worldwide based on citation data. With the new release, a completely revised tool has been published. It is not only based on citation data (bibliometrics), but also Mendeley data (altmetrics). Thus, the institutional impact measurement of the tool has been expanded by focusing on additional status groups besides researchers such as students and librarians. Furthermore, the visualization of the data has been completely updated by improving the operability for the user and including new features such as institutional profle pages. In this paper, we describe the datasets for the current excellencemapping.net tool and the indicators applied. Furthermore, the underlying statistics for the tool and the use of the web application are explained.

Urbanization is accelerating due to economic and societal development. The accurate identification of urban functional zones is significant for urban structure optimization, urban planning, and resource allocation. This paper reviews the scholarly literature on urban functional zone identification. Based on the retrieval results of databases, we analyzed the overview and current status. The identification methods and classification schemes are summarized from the existing research. The following results were obtained: (1) point of interest (POI) data are widely used for functional zone identification; (2) the block is the most common unit for functional zone identification; (3) cluster analysis is the main approach for urban functional zone identification; (4) most of the classification schemes are based on the dominant land use and characteristics of data sources. We predict future trends of urban functional zone identification based on the reviewed literature. Our findings are expected to be valuable for urban studies.

Citation recommendation can help researchers quickly find supplementary or alternative references in massive academic resources. Current research on citation recommendation mainly focuses on the citing papers, resulting in the enormous cited papers are ignored, including the relations among cited papers and their citation context cited in citing papers. Moreover, cited paper’s content is often denoted with its original title and abstract, which is hard to acquire and rarely considers different citation motivations. Furthermore, the most appropriate method for semantic representation of cited papers’ relations and content is uncertain. Therefore, this paper studies citation recommendation from the perspective of semantic representation of cited papers’ relations and content. Firstly, four forms of citation context are designed and extracted as cited papers’ content considering citation motivations, as well as co-citation relationships are extracted as cited papers’ relations. Secondly, 132 methods are designed for generating semantic vector of cited paper, including four network embedding methods, 16 methods by combining four text representation algorithms with four forms of citation content, and 112 fusion methods. Finally, similarity among cited papers is calculated for citation recommendation and a quantitative evaluation method based on link prediction is designed, to find the most appropriate form of citation content and the optimal method. The result shows that doc2vecC (Document to Vector through Corruption) with the form of CS&SS (Current Sentences and Surrounding Sentences) performs best, in which the AUC (Area Under Curve) and MAP (Macro Average Precision) reach 0.877 and 0.889 and have increased by 0.462 and 0.370 compared with the worst-performing method. This performance is slightly improved by parameters adjustment, and a case study is performed whose results have further proved the effectiveness of this method. In addition, among four forms of cited papers’ content, CS&SS performs best in almost all methods. Furthermore, the fusion methods not always perform better than the single methods, where doc2vecC (CS&SS) performs better than the best fusion method GCN (Graph Convolutional Network). These results not only prove the effectiveness of citation recommendation from the perspective of cited paper, but also provide helpful and useful suggestions for method selection and citation content selection. The data and conclusions can be extended to other text mining-related tasks. Simultaneously, it is a preliminary research which needs to be further studied in other domains using emerging semantic representation methods.

The paper presents an information system for calculating the main paper-forming parameters of the pulp for given technological and design parameters of the grinding plant. The operation of the system is based on mathematical regression models of the processes that were obtained in the course of experimental studies of knife sets of various types. As input parameters in these models, the rotor speed, knife gap, concentration and degree of grinding of the mass are used. The output parameters are the grinding time, water retention capacity and average fiber length. The developed information system is a network web application with a modular structure. The modules are united by the main interface for the user. Each module implements a regression model for a specific type of headset. At the moment, the system has two modules for calculating the parameters of a percussion type headset and a headset with a curvilinear shape of knives. In the future, it is planned to add the ability to calculate indicators for headsets of other designs. It will also add the ability to solve optimization problems by finding the minimum or maximum value of the output parameters.

Paper artifacts are contaminated by external factors in the process of preservation such as foxing. For the problem of backward technology of rapid detection of foxing on paper artifacts, a method based on hyperspectral imaging technology is proposed to detect foxing spots on paper artifacts. After selecting the region of interest and obtaining the corresponding average reflectance, the difference in the average reflectance is found after comparing the healthy regions with the diseased regions. Using band operation and minimum noise fraction to observe the characteristics of foxing image, although there is overlap in different parts, the distribution distinction between moldy and healthy regions is obvious; K-nearest neighbor method and BP neural network are applied to establish the spectral discrimination model of paper artifacts with foxing spots, and the overall discrimination rate of the two methods is 73.3% and 85%, respectively. The results show that hyperspectral imaging can be used for the identification of foxing spots, but the distinction between different parts is not good, and the discrimination effect still needs to be improved.

Much literature exists for rock-paper-scissors (RPS) game. It is well known in a single habitat that spatial models are more stable than well-mixed population. However, the mechanism of spatial stabilization has been unclear. In the present article, we study multilayer model of RPS game in a patchy environment; respective patches are set as lattices. The predation probability of one of three species is assumed to be reduced as a parameter. Simulations on two-layer system reveal the opposite result to those on a single-habitat system. Namely, the well-mixed population becomes stable. In contrast, extinction occurs by random migration in spatially-explicit model, when the reduced predation probability is below a certain critical value. The extinction in spatial model is found to be caused by the collapse of a kind of swarm intelligence (SI). In RPS system, large swarms of each species are automatically protected from its predator. Such a self-organized protection is one of the simplest examples of SI. We also discuss some serious problems for random migration.

When COVID-19 was declared as a pandemic by the World Health Organization on 11 March 2020, national governments and health authorities across the world begun considering different preventive measures to fight against the coronavirus outbreak. Researchers and tech companies worldwide have been striving to utilize advanced technologies to aid in the fight against the Covid-19 outbreak. This paper aims to couple multifunction drone with AI to deliver wireless services that will help the fight against the Coronavirus pandemic. The proposed drone-eye-system with its thermal imaging cameras and an AI framework utilizes a Convolutional Neural Network (CNN) with its Modified Artificial Neural Network (MANN) for face mask detection of people wearing masks in public. The system can perform basic diagnostic functions such as elevated body temperatures for helping minimize the risk of spreading the infection through close contact. The AI framework evolve an optimized elevation angle $$\uptheta $$ θ and altitude $${\mathrm{h}}_{\mathrm{t}}$$ h t to enhance wireless connectivity between a drone and a ground station, which in turn leads to better throughput and power consumption. The proposed framework has been developed using the MATLAB toolbox and shows promising results with an accuracy of face mask detection of 82.63%, with an F1-score of 0.98, and an enhanced by 10% link budget parameters.

Social media has been playing a vital importance in information sharing at massive scale due to its easy access, low cost, and faster dissemination of information. Its competence to disseminate the information across a wide audience has raised a critical challenge to determine the social data provenance of digital content. Social Data Provenance describes the origin, derivation process, and transformations of social content throughout its lifecycle. In this paper, we present a Big Social Data Provenance (BSDP) Framework for key-value pair (KVP) database using the novel concept of Zero-Information Loss Database (ZILD). In our proposed framework, a huge volume of social data is first fetched from the social media (Twitter's Network) through live streaming and simultaneously modelled in a KVP database by using a query-driven approach. The proposed framework is capable in capturing, storing, and querying provenance information for different query sets including select, aggregate, standing/historical, and data update (i.e., insert, delete, update) queries on Big Social Data. We evaluate the performance of proposed framework in terms of provenance capturing overhead for different query sets including select, aggregate, and data update queries, and average execution time for various provenance queries.

Motivation In silico saturation mutagenesis (ISM) is a popular approach in computational genomics for calculating feature attributions on biological sequences that proceeds by systematically perturbing each position in a sequence and recording the difference in model output. However, this method can be slow because systematically perturbing each position requires performing a number of forward passes proportional to the length of the sequence being examined. Results In this work, we propose a modification of ISM that leverages the principles of compressed sensing to require only a constant number of forward passes, regardless of sequence length, when applied to models that contain operations with a limited receptive field, such as convolutions. Our method, named Yuzu, can reduce the time that ISM spends in convolution operations by several orders of magnitude and, consequently, Yuzu can speed up ISM on several commonly used architectures in genomics by over an order of magnitude. Notably, we found that Yuzu provides speedups that increase with the complexity of the convolution operation and the length of the sequence being analyzed, suggesting that Yuzu provides large benefits in realistic settings. Availability and implementation We have made this tool available at https://github.com/kundajelab/yuzu.

Motivation Drug repositioning is an attractive alternative to de novo drug discovery due to reduced time and costs to bring drugs to market. Computational repositioning methods, particularly non-black-box methods that can account for and predict a drug’s mechanism, may provide great benefit for directing future development. By tuning both data and algorithm to utilize relationships important to drug mechanisms, a computational repositioning algorithm can be trained to both predict and explain mechanistically novel indications. Results In this work, we examined the 123 curated drug mechanism paths found in the drug mechanism database (DrugMechDB) and after identifying the most important relationships, we integrated 18 data sources to produce a heterogeneous knowledge graph, MechRepoNet, capable of capturing the information in these paths. We applied the Rephetio repurposing algorithm to MechRepoNet using only a subset of relationships known to be mechanistic in nature and found adequate predictive ability on an evaluation set with AUROC value of 0.83. The resulting repurposing model allowed us to prioritize paths in our knowledge graph to produce a predicted treatment mechanism. We found that DrugMechDB paths, when present in the network were rated highly among predicted mechanisms. We then demonstrated MechRepoNet’s ability to use mechanistic insight to identify a drug’s mechanistic target, with a mean reciprocal rank of 0.525 on a test set of known drug–target interactions. Finally, we walked through repurposing examples of the anti-cancer drug imatinib for use in the treatment of asthma, and metolazone for use in the treatment of osteoporosis, to demonstrate this method’s utility in providing mechanistic insight into repurposing predictions it provides. Availability and implementation The Python code to reproduce the entirety of this analysis is available at: https://github.com/SuLab/MechRepoNet (archived at https://doi.org/10.5281/zenodo.6456335). Supplementary information Supplementary data are available at Bioinformatics online.

Motivation The development of an open-source platform to predict protein 1D features and 3D structure is an important task. In this paper, we report an open-source toolkit for protein 3D structure modeling, named OPUS-X. It contains three modules: OPUS-TASS2, which predicts protein torsion angles, secondary structure and solvent accessibility; OPUS-Contact, which measures the distance and orientation information between different residue pairs; and OPUS-Fold2, which uses the constraints derived from the first two modules to guide folding. Results OPUS-TASS2 is an upgraded version of our previous method OPUS-TASS. OPUS-TASS2 integrates protein global structure information and significantly outperforms OPUS-TASS. OPUS-Contact combines multiple raw co-evolutionary features with protein 1D features predicted by OPUS-TASS2, and delivers better results than the open-source state-of-the-art method trRosetta. OPUS-Fold2 is a complementary version of our previous method OPUS-Fold. OPUS-Fold2 is a gradient-based protein folding framework based on the differentiable energy terms in opposed to OPUS-Fold that is a sampling-based method used to deal with the non-differentiable terms. OPUS-Fold2 exhibits comparable performance to the Rosetta folding protocol in trRosetta when using identical inputs. OPUS-Fold2 is written in Python and TensorFlow2.4, which is user-friendly to any source-code-level modification. Availabilityand implementation The code and pre-trained models of OPUS-X can be downloaded from https://github.com/OPUS-MaLab/opus_x. Supplementary information Supplementary data are available at Bioinformatics online.

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.

Background:The COVID-19 pandemic has changed various spheres of healthcare. The general practitioners (GPs) have widely replaced face-to-face consultations with telephone or video consultation (VC) to reduce the risk of COVID-19 transmission. Using video consultations for health service deliveries is an entirely new way of practicing for many GPs. Yet, this transition process has largely been carried out with no formal guidelines, which may have caused implementation barriers. This study presents a rapid-cycle co-production approach to develop a guide to assist VC implementation in general practice.Objective:The aim of this paper was to describe the developmental phases of the guide and to summarize the evaluation made by general practice users.Methods:The development of a guide for VC in general practice was structured as a stepped process based on co-production and prototyping processes. We used an iterative framework based on rapid qualitative analyses and interdisciplinary collaboration. Thus, the guide was developed in small, repeated cycles of development, implementation, evaluation, and adaptation with a continuous exchange between research and practice. The data collection process was structured in three main phases. First, we made a literature review and qualitative prestudies. Second, we facilitated co-production with stakeholders through four workshops with GPs, a group interview with patient representatives, and individual revisions by general practitioners. Third, nationwide testing was conducted in five general practice clinics and was followed by an evaluation of the guide through interviews with GPs.Results:A rapid-cycle co-production approach was used to explore the needs in general practice in connection with the implementation of VC and to develop useful, relevant, and easily understandable guiding materials. Our findings suggest that a guide for VC should include advice and recommendations regarding the organization of VC, the technical setup, the appropriate target groups, patients’ use of VC, the performance of VC, and the arrangement of booking.Conclusions:The combination of co-production, prototyping, small iterations, and rapid data analysis is a suitable approach when contextually rich, hands-on guide materials are urgently needed. Moreover, this method could provide an efficient way of developing relevant guide materials for general practice to aid the implementation of new technology beyond pandemic times. However, their potential can only be realized if the generated materials are adopted and sustained in practice. Hence, such a developmental approach should involve a plan for the continued engagement of stakeholders. Background: The COVID-19 pandemic has changed various spheres of health care. General practitioners (GPs) have widely replaced face-to-face consultations with telephone or video consultations (VCs) to reduce the risk of COVID-19 transmission. Using VCs for health service delivery is an entirely new way of practicing for many GPs. However, this transition process has largely been conducted with no formal guidelines, which may have caused implementation barriers. This study presents a rapid cycle coproduction approach for developing a guide to assist VC implementation in general practice. Objective: The aim of this paper is to describe the developmental phases of the VC guide to assist general practices in implementing VCs and summarize the evaluation made by general practice users. Methods: The development of a guide for VC in general practice was structured as a stepped process based on the coproduction and prototyping processes. We used an iterative framework based on rapid qualitative analyses and interdisciplinary collaborations. Thus, the guide was developed in small, repeated cycles of development, implementation, evaluation, and adaptation, with a continuous exchange between research and practice. The data collection process was structured in 3 main phases. First, we conducted a literature review, recorded observations, and held informal and semistructured interviews. Second, we facilitated coproduction with stakeholders through 4 workshops with GPs, a group interview with patient representatives, and individual revisions by GPs. Third, nationwide testing was conducted in 5 general practice clinics and was followed by an evaluation of the guide through interviews with GPs. Results: A rapid cycle coproduction approach was used to explore the needs of general practice in connection with the implementation of VC and to develop useful, relevant, and easily understandable guiding materials. Our findings suggest that a guide for VCs should include advice and recommendations regarding the organization of VCs, the technical setup, the appropriate target groups, patients' use of VCs, the performance of VCs, and the arrangements for booking a VC. Conclusions: The combination of coproduction, prototyping, small iterations, and rapid data analysis is a suitable approach when contextually rich, hands-on guide materials are urgently needed. Moreover, this method could provide an efficient way of developing relevant guide materials for general practice to aid the implementation of new technology beyond the pandemic period.

Pattern mining from graph transactional data (GTD) is an active area of research with applications in the domains of bioinformatics, chemical informatics and social networks. Existing works address the problem of mining frequent subgraphs from GTD. However, the knowledge concerning the coverage aspect of a set of subgraphs is also valuable for improving the performance of several applications. In this regard, we introduce the notion of subgraph coverage patterns (SCPs). Given a GTD, a subgraph coverage pattern is a set of subgraphs subject to relative frequency, coverage and overlap constraints provided by the user. We propose the Subgraph ID-based Flat Transactional (SIFT) framework for the efficient extraction of SCPs from a given GTD. Our performance evaluation using three real datasets demonstrates that our proposed SIFT framework is indeed capable of efficiently extracting SCPs from GTD. Furthermore, we demonstrate the effectiveness of SIFT through a case study in computer-aided drug design.

Summary Multiple sequence alignment is an initial step in many bioinformatics pipelines, including phylogeny estimation, protein structure prediction and taxonomic identification of reads produced in amplicon or metagenomic datasets, etc. Yet, alignment estimation is challenging on datasets that exhibit substantial sequence length heterogeneity, and especially when the datasets have fragmentary sequences as a result of including reads or contigs generated by next-generation sequencing technologies. Here, we examine techniques that have been developed to improve alignment estimation when datasets contain substantial numbers of fragmentary sequences. We find that MAGUS, a recently developed MSA method, is fairly robust to fragmentary sequences under many conditions, and that using a two-stage approach where MAGUS is used to align selected ‘backbone sequences’ and the remaining sequences are added into the alignment using ensembles of Hidden Markov Models further improves alignment accuracy. The combination of MAGUS with the ensemble of eHMMs (i.e. MAGUS+eHMMs) clearly improves on UPP, the previous leading method for aligning datasets with high levels of fragmentation. Availability and implementation UPP is available on https://github.com/smirarab/sepp, and MAGUS is available on https://github.com/vlasmirnov/MAGUS. MAGUS+eHMMs can be performed by running MAGUS to obtain the backbone alignment, and then using the backbone alignment as an input to UPP. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation Gene expression-based multiclass prediction, such as tumor subtyping, is a non-trivial bioinformatic problem. Most classifier methods operate by comparing expression levels relative to other samples. Methods that base predictions on the expression pattern within a sample have been proposed as an alternative. As these methods are invariant to the cohort composition and can be applied to a sample in isolation, they can collectively be termed single sample predictors (SSP). Such predictors could potentially be used for preprocessing-free classification of new samples and be built to function across different expression platforms where proper batch and dataset normalization is challenging. Here, we evaluate the behavior of several multiclass SSPs based on binary gene-pair rules (k-Top Scoring Pairs, Absolute Intrinsic Molecular Subtyping and a new Random Forest approach) and compare them to centroids built with centered or raw expression values, with the criteria that an optimal predictor should have high accuracy, overcome differences in tumor purity, be robust across expression platforms and provide an informative prediction output score. Results We found that gene-pair-based SSPs showed excellent performance on many expression-based classification tasks. The three methods differed in prediction score output, handling of tied scores and behavior in low purity samples. The k-Top Scoring Pairs and Random Forest approach both achieved high classification accuracy while providing an informative prediction score. Although gene-pair-based SSPs have been touted as being cross-platform compatible (through training on mixed platform data), out-of-the-box compatibility with a new dataset remains a potential issue that warrants cohort-to-cohort verification. Availability and implementation Our R package ‘multiclassPairs’ (https://cran.r-project.org/package=multiclassPairs) (https://doi.org/10.1093/bioinformatics/btab088) is freely available and enables easy training, prediction, and visualization using the gene-pair rule-based Random Forest SSP method and provides additional multiclass functionalities to the switchBox k-Top-Scoring Pairs package. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation In the last decade, de novo protein structure prediction accuracy for individual proteins has improved significantly by utilising deep learning (DL) methods for harvesting the co-evolution information from large multiple sequence alignments (MSAs). The same approach can, in principle, also be used to extract information about evolutionary-based contacts across protein–protein interfaces. However, most earlier studies have not used the latest DL methods for inter-chain contact distance prediction. This article introduces a fold-and-dock method based on predicted residue-residue distances with trRosetta. Results The method can simultaneously predict the tertiary and quaternary structure of a protein pair, even when the structures of the monomers are not known. The straightforward application of this method to a standard dataset for protein–protein docking yielded limited success. However, using alternative methods for generating MSAs allowed us to dock accurately significantly more proteins. We also introduced a novel scoring function, PconsDock, that accurately separates 98% of correctly and incorrectly folded and docked proteins. The average performance of the method is comparable to the use of traditional, template-based or ab initio shape-complementarity-only docking methods. Moreover, the results of conventional and fold-and-dock approaches are complementary, and thus a combined docking pipeline could increase overall docking success significantly. This methodology contributed to the best model for one of the CASP14 oligomeric targets, H1065. Availability and implementation All scripts for predictions and analysis are available from https://github.com/ElofssonLab/bioinfo-toolbox/ and https://gitlab.com/ElofssonLab/benchmark5/. All models joined alignments, and evaluation results are available from the following figshare repository https://doi.org/10.6084/m9.figshare.14654886.v2. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation Differential network inference is a fundamental and challenging problem to reveal gene interactions and regulation relationships under different conditions. Many algorithms have been developed for this problem; however, they do not consider the differences between the importance of genes, which may not fit the real-world situation. Different genes have different mutation probabilities, and the vital genes associated with basic life activities have less fault tolerance to mutation. Equally treating all genes may bias the results of differential network inference. Thus, it is necessary to consider the importance of genes in the models of differential network inference. Results Based on the Gaussian graphical model with adaptive gene importance regularization, we develop a novel Importance-Penalized Joint Graphical Lasso method (IPJGL) for differential network inference. The presented method is validated by the simulation experiments as well as the real datasets. Furthermore, to precisely evaluate the results of differential network inference, we propose a new metric named APC2 for the differential levels of gene pairs. We apply IPJGL to analyze the TCGA colorectal and breast cancer datasets and find some candidate cancer genes with significant survival analysis results, including SOST for colorectal cancer and RBBP8 for breast cancer. We also conduct further analysis based on the interactions in the Reactome database and confirm the utility of our method. Availability and implementation R source code of Importance-Penalized Joint Graphical Lasso is freely available at https://github.com/Wu-Lab/IPJGL. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. The task of imputing single-cell (methylation) data requires models to build an understanding of underlying biological processes. Results We adapt the transformer neural network architecture to operate on methylation matrices through combining axial attention with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art performances on a wide range of scBS-seq and scRRBS-seq datasets. Furthermore, we demonstrate the interpretability of CpG Transformer and illustrate its rapid transfer learning properties, allowing practitioners to train models on new datasets with a limited computational and time budget. Availability and implementation CpG Transformer is freely available at https://github.com/gdewael/cpg-transformer. Supplementary information Supplementary data are available at Bioinformatics online.

The digital transformation offers new opportunities for organizations to expand their existing service portfolio in order to achieve competitive advantages. A popular way to create new customer value is the offer of analytics-based services (ABS)—services that apply analytical methods to data to empower customers to make better decisions and to solve complex problems. However, research still lacks to provide a profound conceptualization of this novel service type. Similarly, actionable insights on how to purposefully establish ABS in the market to enrich the service portfolio remain scarce. We perform a cluster analysis of 105 ABS and triangulate it with a revelatory case study to identify four generic ABS archetypes and to unveil their specific service objectives and characteristics. We also isolate essential factors that shape decision-making regarding the choice of adequate archetypes and subsequent transitions between them. The detailed characterization of different ABS types contributes to a more profound theorizing process on ABS as well as provides a systematization for strategic opportunities to enrich service portfolios in practice.

Motivation The objective is to diagnose dynamics perturbations caused by amino-acid mutations as prerequisite to assess protein functional health or drug failure, simply using network models of protein X-ray structures. Results We find that the differences in the allocation of the atomic interactions of each amino acid to 1D, 2D, 3D, 4D structural levels between variants structurally robust, recover experimental dynamic perturbations. The allocation measure validated on two B-pentamers variants of AB5 toxins having 17 mutations, also distinguishes dynamic perturbations of pathogenic and non-pathogenic Transthyretin single-mutants. Finally, the main proteases of the coronaviruses SARS-CoV and SARS-CoV-2 exhibit changes in the allocation measure, raising the possibility of drug failure despite the main proteases structural similarity. Availability and implementation The Python code used for the production of the results is available at github.com/lorpac/protein_partitioning_atomic_contacts. The authors will run the analysis on any PDB structures of protein variants upon request. Supplementary information Supplementary data are available at Bioinformatics online.

MotivationClustering is a fundamental task in the analysis of nucleotide sequences. Despite the exponential increase in the size of sequence databases of homologous genes, few methods exist to cluster divergent sequences. Traditional clustering methods have mostly focused on optimizing high speed clustering of highly similar sequences. We develop a phylogenetic clustering method which infers ancestral sequences for a set of initial clusters and then uses a greedy algorithm to cluster sequences.ResultsWe describe a clustering program AncestralClust, which is developed for clustering divergent sequences. We compare this method with other state-of-the-art clustering methods using datasets of homologous sequences from different species. We show that, in divergent datasets, AncestralClust has higher accuracy and more even cluster sizes than current popular methods.Availability and implementationAncestralClust is an Open Source program available at https://github.com/lpipes/ancestralclust.Contactlpipes@berkeley.eduSupplementary informationSupplementary figures and table are available online.

Motivation The acid dissociation constant (pKa) is a critical parameter to reflect the ionization ability of chemical compounds and is widely applied in a variety of industries. However, the experimental determination of pKa is intricate and time-consuming, especially for the exact determination of micro-pKa information at the atomic level. Hence, a fast and accurate prediction of pKa values of chemical compounds is of broad interest. Results Here, we compiled a large-scale pKa dataset containing 16 595 compounds with 17 489 pKa values. Based on this dataset, a novel pKa prediction model, named Graph-pKa, was established using graph neural networks. Graph-pKa performed well on the prediction of macro-pKa values, with a mean absolute error around 0.55 and a coefficient of determination around 0.92 on the test dataset. Furthermore, combining multi-instance learning, Graph-pKa was also able to automatically deconvolute the predicted macro-pKa into discrete micro-pKa values. Availability and implementation The Graph-pKa model is now freely accessible via a web-based interface (https://pka.simm.ac.cn/). Supplementary information Supplementary data are available at Bioinformatics online.

Motivation Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. Results To address this problem, we developed a novel clustering approach called ‘metagenomic clustering by reference library’ (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed ‘signatures’, are iteratively clustered in a greedy fashion, retaining at each step the reference genes yielding the lowest E values, and terminating when signatures of remaining reference genes have a minimal overlap. The outcome of this computation is a non-redundant list of reference genes homologous to minimally overlapping sets of contigs, representing potential candidates for gene families present in the metagenome. Unlike metagenomic clustering methods, there is no need for contigs to overlap to be associated with a cluster, enabling MCRL to draw on more information encoded in the metagenome when computing tentative gene families. We demonstrate how MCRL can be used to extract candidate viral gene families from an oral metagenome and an oral virome that otherwise could not be determined using standard approaches. We evaluate the sensitivity, accuracy and robustness of our proposed method for the viral case study and compare it with existing analysis approaches. Availability and implementation https://github.com/a-tadmor/MCRL. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation Recent advancements in fluorescence in situ hybridization (FISH) techniques enable them to concurrently obtain information on the location and gene expression of single cells. A key question in the initial analysis of such spatial transcriptomics data is the assignment of cell types. To date, most studies used methods that only rely on the expression levels of the genes in each cell for such assignments. To fully utilize the data and to improve the ability to identify novel sub-types, we developed a new method, FICT, which combines both expression and neighborhood information when assigning cell types. Results FICT optimizes a probabilistic function that we formalize and for which we provide learning and inference algorithms. We used FICT to analyze both simulated and several real spatial transcriptomics data. As we show, FICT can accurately identify cell types and sub-types, improving on expression only methods and other methods proposed for clustering spatial transcriptomics data. Some of the spatial sub-types identified by FICT provide novel hypotheses about the new functions for excitatory and inhibitory neurons. Availability and implementation FICT is available at: https://github.com/haotianteng/FICT. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid and accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) is time-consuming, low throughput and viable only for cultivable bacteria. Machine learning methods may pave the way for automated AMR prediction based on genomic data of the bacteria. However, comparing different machine learning methods for the prediction of AMR based on different encodings and whole-genome sequencing data without previously known knowledge remains to be done. Results In this study, we evaluated logistic regression (LR), support vector machine (SVM), random forest (RF) and convolutional neural network (CNN) for the prediction of AMR for the antibiotics ciprofloxacin, cefotaxime, ceftazidime and gentamicin. We could demonstrate that these models can effectively predict AMR with label encoding, one-hot encoding and frequency matrix chaos game representation (FCGR encoding) on whole-genome sequencing data. We trained these models on a large AMR dataset and evaluated them on an independent public dataset. Generally, RFs and CNNs perform better than LR and SVM with AUCs up to 0.96. Furthermore, we were able to identify mutations that are associated with AMR for each antibiotic. Availability and implementation Source code in data preparation and model training are provided at GitHub website (https://github.com/YunxiaoRen/ML-iAMR). Supplementary information Supplementary data are available at Bioinformatics online.

Background The dramatic increase in complexity and volume of health data has challenged traditional health systems to deliver useful information to their users. The novel coronavirus disease 2019 (COVID-19) pandemic has further exacerbated this problem and demonstrated the critical need for the 21st century approach. This approach needs to ingest relevant, diverse data sources, analyze them, and generate appropriate health intelligence products that enable users to take more effective and efficient actions for their specific challenges. Objectives This article characterizes the Health Intelligence Atlas (HI-Atlas) development and implementation to produce Public Health Intelligence (PHI) that supports identifying and prioritizing high-risk communities by public health authorities. The HI-Atlas moves from post hoc observations to a proactive model-based approach for preplanning COVID-19 vaccine preparedness, distribution, and assessing the effectiveness of those plans. Results Details are presented on how the HI-Atlas merged traditional surveillance data with social intelligence multidimensional data streams to produce the next level of health intelligence. Two-model use cases in a large county demonstrate how the HI-Atlas produced relevant PHI to inform public health decision makers to (1) support identification and prioritization of vulnerable communities at risk for COVID-19 spread and vaccine hesitancy, and (2) support the implementation of a generic model for planning equitable COVID-19 vaccine preparedness and distribution. Conclusion The scalable models of data sources, analyses, and smart hybrid data layer visualizations implemented in the HI-Atlas are the Health Intelligence tools designed to support real-time proactive planning and monitoring for COVID-19 vaccine preparedness and distribution in counties and states.

Motivation Protein–protein interaction (PPI), as a relative property, is determined by two binding proteins, which brings a great challenge to design an expert model with an unbiased learning architecture and a superior generalization performance. Additionally, few efforts have been made to allow PPI predictors to discriminate between relative properties and intrinsic properties. Results We present a sequence-based approach, DeepTrio, for PPI prediction using mask multiple parallel convolutional neural networks. Experimental evaluations show that DeepTrio achieves a better performance over several state-of-the-art methods in terms of various quality metrics. Besides, DeepTrio is extended to provide additional insights into the contribution of each input neuron to the prediction results. Availability and implementation We provide an online application at http://bis.zju.edu.cn/deeptrio. The DeepTrio models and training data are deposited at https://github.com/huxiaoti/deeptrio.git. Supplementary information Supplementary data are available at Bioinformatics online.

Technology integration within instructional practices is an essential element in the preparation of teachers. However, expectations that a single course or hopes that technology infusion will spontaneously occur are not enough to prepare teacher candidates to integrate technology in meaningful ways. In the absence of a required educational technology course for all initial licensure candidates, an educator preparation program in the Midwest sought creative solutions to meet accreditation and clinical placement expectations regarding candidate preparation to integrate technology. This report from the field discusses the iterative process to develop a comprehensive micro-credentialing system aligned with the ISTE standards for educators. The micro-credentials provide candidates opportunities to apply and model technology use within courses and throughout their program. Feedback from stakeholders indicated both possibilities and potential challenges in the adoption of the system. This feedback has led to further development of the micro-credentialing system.

The image biomarkers standardization initiative (IBSI) was formed to address the standardization of extraction of quantifiable imaging metrics. Despite its effort, there remains a lack of consensus or established guidelines regarding radiomic feature terminology, the underlying mathematics and their implementation across various software programs. This creates a scenario where features extracted using different toolboxes cannot be used to build or validate the same model leading to a non-generalization of radiomic results. In this study, IBSI-established phantom and benchmark values were used to compare the variation of the radiomic features while using 6 publicly available software programs and 1 in-house radiomics pipeline. All IBSI-standardized features (11 classes, 173 in total) were extracted. The relative differences between the extracted feature values from the different software programs and the IBSI benchmark values were calculated to measure the inter-software agreement. To better understand the variations, features are further grouped into 3 categories according to their properties: 1) morphology, 2) statistic/histogram and 3)texture features. While a good agreement was observed for a majority of radiomics features across the various tested programs, relatively poor agreement was observed for morphology features. Significant differences were also found in programs that use different gray-level discretization approaches. Since these software programs do not include all IBSI features, the level of quantitative assessment for each category was analyzed using Venn and UpSet diagrams and quantified using two ad hoc metrics. Morphology features earned lowest scores for both metrics, indicating that morphological features are not consistently evaluated among software programs. We conclude that radiomic features calculated using different software programs may not be interchangeable. Further studies are needed to standardize the workflow of radiomic feature extraction. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10278-021-00506-6.

Fuzzy soft graphs are effective mathematical tools that are used to model the vagueness of the real world. A fuzzy soft graph is a fusion of the fuzzy soft set and the graph model and is widely used across different fields. In this current research, the concept of picture fuzzy soft graphs is presented by combining the theory of picture soft sets with graphs. The introduction of this new picture fuzzy soft graphs is an emerging concept that can be rather developed into various graph theoretical concepts. Since soft sets are most usable in real-life applications, the newly combined concepts of the picture and fuzzy soft sets will lead to many possible applications in the fuzzy set theoretical area by adding extra fuzziness in analyzing. The notions of picture soft graphs, strong and complete picture soft fuzzy graphs, a few types of product picture fuzzy soft graphs, and regular, totally regular picture fuzzy soft graphs are discussed and validated using real-world scenarios. In addition, an application of decision-making for medical diagnosis in the current COVID scenario using the picture fuzzy soft graph has been illustrated.

Maximum intensity projection (MIP) technology is a computer visualization method that projects three-dimensional spatial data on a visualization plane. According to the specific purposes, the specific lab thickness and direction can be selected. This technology can better show organs, such as blood vessels, arteries, veins, and bronchi and so forth, from different directions, which could bring more intuitive and comprehensive results for doctors in the diagnosis of related diseases. However, in this traditional projection technology, the details of the small projected target are not clearly visualized when the projected target is not much different from the surrounding environment, which could lead to missed diagnosis or misdiagnosis. Therefore, it is urgent to develop a new technology that can better and clearly display the angiogram. However, to the best of our knowledge, research in this area is scarce. To fill this gap in the literature, in the present study, we propose a new method based on the hybrid of convolutional neural network (CNN) and radial basis function neural network (RBFNN) to synthesize the projection image. We first adopted the U-net to obtain feature or enhanced images to be projected; subsequently, the RBF neural network performed further synthesis processing for these data; finally, the projection images were obtained. For experimental data, in order to increase the robustness of the proposed algorithm, the following three different types of datasets were adopted: the vascular projection of the brain, the bronchial projection of the lung parenchyma, and the vascular projection of the liver. In addition, radiologist evaluation and five classic metrics of image definition were implemented for effective analysis. Finally, compared to the traditional MIP technology and other structures, the use of a large number of different types of data and superior experimental results proved the versatility and robustness of the proposed method.

Motivation Single-cell transcriptomics profiling technologies enable genome-wide gene expression measurements in individual cells but can currently only provide a static snapshot of cellular transcriptional states. RNA velocity analysis can help infer cell state changes using such single-cell transcriptomics data. To interpret these cell state changes inferred from RNA velocity analysis as part of underlying cellular trajectories, current approaches rely on visualization with principal components, t-distributed stochastic neighbor embedding and other 2D embeddings derived from the observed single-cell transcriptional states. However, these 2D embeddings can yield different representations of the underlying cellular trajectories, hindering the interpretation of cell state changes. Results We developed VeloViz to create RNA velocity-informed 2D and 3D embeddings from single-cell transcriptomics data. Using both real and simulated data, we demonstrate that VeloViz embeddings are able to capture underlying cellular trajectories across diverse trajectory topologies, even when intermediate cell states may be missing. By considering the predicted future transcriptional states from RNA velocity analysis, VeloViz can help visualize a more reliable representation of underlying cellular trajectories. Availability and implementation Source code is available on GitHub (https://github.com/JEFworks-Lab/veloviz) and Bioconductor (https://bioconductor.org/packages/veloviz) with additional tutorials at https://JEF.works/veloviz/. Datasets used can be found on Zenodo (https://doi.org/10.5281/zenodo.4632471). Supplementary information Supplementary data are available at Bioinformatics online.

Fuzzy mixed graph (FMG) can be used to model some graphical intercommunication network systems if there are many directed and undirected relations between some vertices. In inverse fuzzy graph, the membership value of edges are greater than or equal to the minimum of the membership value of the corresponding vertices. In inverse fuzzy mixed graph (IFMG), directed and undirected relations exist between some vertices and it can be used to analyze many graphical problems of real life such that the membership values of edges are greater than or equal to the minimum of the membership value of the corresponding pair of vertices. In this article, the concept of IFMG is introduced first with some of its properties. Then some isomorphic properties are studied and complement of IFMG is given. Different types of operations like union, intersection, product and join between two IFMGs are defined and investigated some of their related results. An algorithm of the proposed method is executed to identify some vertices. An application is depicted using the concept IFMG to examine the order of vertices in a social network group according to communication gaps.

Motivation The automatic discovery of sparse biomarkers that are associated with an outcome of interest is a central goal of bioinformatics. In the context of high-throughput sequencing (HTS) data, and compositional data (CoDa) more generally, an important class of biomarkers are the log-ratios between the input variables. However, identifying predictive log-ratio biomarkers from HTS data is a combinatorial optimization problem, which is computationally challenging. Existing methods are slow to run and scale poorly with the dimension of the input, which has limited their application to low- and moderate-dimensional metagenomic datasets. Results Building on recent advances from the field of deep learning, we present CoDaCoRe, a novel learning algorithm that identifies sparse, interpretable and predictive log-ratio biomarkers. Our algorithm exploits a continuous relaxation to approximate the underlying combinatorial optimization problem. This relaxation can then be optimized efficiently using the modern ML toolbox, in particular, gradient descent. As a result, CoDaCoRe runs several orders of magnitude faster than competing methods, all while achieving state-of-the-art performance in terms of predictive accuracy and sparsity. We verify the outperformance of CoDaCoRe across a wide range of microbiome, metabolite and microRNA benchmark datasets, as well as a particularly high-dimensional dataset that is outright computationally intractable for existing sparse log-ratio selection methods. Availability and implementation The CoDaCoRe package is available at https://github.com/egr95/R-codacore. Code and instructions for reproducing our results are available at https://github.com/cunningham-lab/codacore. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation Each year, the number of published bulk and single-cell RNA-seq datasets is growing exponentially. Studies analyzing such data are commonly looking at gene-level differences, while the collected RNA-seq data inherently represents reads of transcript isoform sequences. Utilizing transcriptomic quantifiers, RNA-seq reads can be attributed to specific isoforms, allowing for analysis of transcript-level differences. A differential transcript usage (DTU) analysis is testing for proportional differences in a gene’s transcript composition, and has been of rising interest for many research questions, such as analysis of differential splicing or cell-type identification. Results We present the R package DTUrtle, the first DTU analysis workflow for both bulk and single-cell RNA-seq datasets, and the first package to conduct a ‘classical’ DTU analysis in a single-cell context. DTUrtle extends established statistical frameworks, offers various result aggregation and visualization options and a novel detection probability score for tagged-end data. It has been successfully applied to bulk and single-cell RNA-seq data of human and mouse, confirming and extending key results. In addition, we present novel potential DTU applications like the identification of cell-type specific transcript isoforms as biomarkers. Availability and implementation The R package DTUrtle is available at https://github.com/TobiTekath/DTUrtle with extensive vignettes and documentation at https://tobitekath.github.io/DTUrtle/. Supplementary information Supplementary data are available at Bioinformatics online.

The identification of extreme rare events is a challenge that appears in several real-world contexts, from screening for solo perpetrators to the prediction of failures in industrial production. In this article, we explain the challenge and present a new methodology for addressing it, a methodology that may be considered in terms of features engineering. This methodology, which is based on Jaynes inferential approach, is tested on a dataset dealing with failures in production in the pulp-and-paper industry. The results are discussed in the context of the benefits of using the approach for features engineering in practical contexts involving measurable risks.

Motivation Modeling single-cell gene expression trends along cell pseudotime is a crucial analysis for exploring biological processes. Most existing methods rely on nonparametric regression models for their flexibility; however, nonparametric models often provide trends too complex to interpret. Other existing methods use interpretable but restrictive models. Since model interpretability and flexibility are both indispensable for understanding biological processes, the single-cell field needs a model that improves the interpretability and largely maintains the flexibility of nonparametric regression models. Results Here, we propose the single-cell generalized trend model (scGTM) for capturing a gene’s expression trend, which may be monotone, hill-shaped or valley-shaped, along cell pseudotime. The scGTM has three advantages: (i) it can capture non-monotonic trends that are easy to interpret, (ii) its parameters are biologically interpretable and trend informative, and (iii) it can flexibly accommodate common distributions for modeling gene expression counts. To tackle the complex optimization problems, we use the particle swarm optimization algorithm to find the constrained maximum likelihood estimates for the scGTM parameters. As an application, we analyze several single-cell gene expression datasets using the scGTM and show that scGTM can capture interpretable gene expression trends along cell pseudotime and reveal molecular insights underlying biological processes. Availability and implementation The Python package scGTM is open-access and available at https://github.com/ElvisCuiHan/scGTM. Supplementary information Supplementary data are available at Bioinformatics online.

Historically, identifying carcinogens has relied primarily on tumor studies in rodents, which require enormous resources in both money and time. In silico models have been developed for predicting rodent carcinogens but have not yet found general regulatory acceptance, in part due to the lack of a generally accepted protocol for performing such an assessment as well as limitations in predictive performance and scope. There remains a need for additional, improved in silico carcinogenicity models, especially ones that are more human-relevant, for use in research and regulatory decision-making. As part of an international effort to develop in silico toxicological protocols, a consortium of toxicologists, computational scientists, and regulatory scientists across several industries and governmental agencies evaluated the extent to which in silico models exist for each of the recently defined 10 key characteristics (KCs) of carcinogens. This position paper summarizes the current status of in silico tools for the assessment of each KC and identifies the data gaps that need to be addressed before a comprehensive in silico carcinogenicity protocol can be developed for regulatory use.

[EN] Emerging Industry 4.0 applications require ever-increasing amounts of data and new sources of information to more accurately characterize the different processes of a production line. Industrial Internet of Things (IIoT) technologies, and in particular Wireless Sensor Networks (WSNs), allow a large amount of data to be digitized at a low energy cost, thanks to their easy scalability and the creation of meshed networks to cover larger areas. In industry, data acquisition systems must meet certain reliability and robustness requirements, since other systems such as predictive maintenance or the digital twin, which represents a virtual mapping of the system with which to interact without the need to alter the actual installation, may depend on it. Thanks to the IEEE 802.15.4e standard and the use of Time-Slotted Channel Hopping (TSCH) as the medium access mechanism and IPv6 Routing Protocol for Low-Power and Lossy Networks (RPL) as the routing protocol, it is possible to deploy WSNs with high reliability, autonomy, and minimal need for re-configuration. One of the drawbacks of this communication architecture is the low efficiency of its deployment process, during which it may take a long time to synchronize and connect all the devices in a network. This paper proposes an analytical model to characterize the process for the creation of downstream routes in RPL, whose transmission of multi-hop messages can present complications in scenarios with a multitude of interfering nodes and resource allocation based on minimal IPv6 over the TSCH mode of IEEE 802.15.4e (6TiSCH). This type of multi-hop message exchange has a different behaviour than the multicast control messages exchanged during the synchronization phase and the formation of upstream routes, since the number of interfering nodes changes in each retransmission., The research leading to these results is part of the i4Q project that has received funding from the European Union's Horizon 2020 Research and Innovation Programme, under Grant Agreement No. 958205.