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Objective The purpose of this study was to develop a natural language processing (NLP) pipeline to identify incidental thyroid nodules (ITNs) meeting criteria for sonographic follow-up and to assess both adherence rates to white paper recommendations and downstream outcomes related to these incidental findings. Methods 21583 non-contrast chest CT reports from 2017 and 2018 were retrospectively evaluated to identify reports which included either an explicit recommendation for thyroid ultrasound, a description of a nodule ≥ 1.5 cm, or description of a nodule with suspicious features. Reports from 2018 were used to train an NLP algorithm called fastText for automated identification of such reports. Algorithm performance was then evaluated on the 2017 reports. Next, any patient from 2017 with a report meeting criteria for ultrasound follow-up was further evaluated with manual chart review to determine follow-up adherence rates and nodule-related outcomes. Results NLP identified reports with ITNs meeting criteria for sonographic follow-up with an accuracy of 96.5% (95% CI 96.2-96.7) and sensitivity of 92.1% (95% CI 89.8-94.3). In 10006 chest CTs from 2017, ITN follow-up ultrasound was indicated according to white paper criteria in 81 patients (0.8%), explicitly recommended in 46.9% (38/81) of patients, and obtained in less than half of patients in which it was appropriately recommended (17/35, 48.6%). Discussion NLP accurately identified chest CT reports meeting criteria for ITN ultrasound follow-up. Radiologist adherence to white paper guidelines and subsequent referrer adherence to radiologist recommendations showed room for improvement.

The accuracy of a predictive system is critical for predictive maintenance and to support the right decisions at the right times. Statistical models, such as ARIMA and SARIMA, are unable to describe the stochastic nature of the data. Neural networks, such as long short-term memory (LSTM) and the gated recurrent unit (GRU), are good predictors for univariate and multivariate data. The present paper describes a case study where the performances of long short-term memory and gated recurrent units are compared, based on different hyperparameters. In general, gated recurrent units exhibit better performance, based on a case study on pulp paper presses. The final result demonstrates that, to maximize the equipment availability, gated recurrent units, as demonstrated in the paper, are the best options.

Performance/security trade-off is widely noticed in CFI research, however, we observe that not every CFI scheme is subject to the trade-off. Motivated by the key observation, we ask three questions: ➊ does trade-off really exist in different CFI schemes? ➋ if trade-off do exist, how do previous works comply with it? ➌ how can it inspire future research? Although the three questions probably cannot be directly answered, they are inspiring. We find that a deeper understanding of the nature of the trade-off will help answer the three questions. Accordingly, we proposed theGPTconjecture to pinpoint the trade-off in designing CFI schemes, which says that at most two out of three properties (fine granularity, acceptable performance, and preventive protection) could be achieved.

International audience; Despite predictions of the paperless office, global demand for printing and writing paper remains strong, and paper appears to be here to stay for some time. Not only firms, but also governments, libraries, and archives are in possession of large collections of legacy documents that still must be sorted and scanned. In this study, terahertz-based techniques are demonstrated to address several routine tasks related to the automated paper handling of unsorted legacy documents. Specifically, we demonstrate terahertz-based counting of the number of sheets in unconsolidated paper stacks, as well as locating stapled documents buried in paper stacks.

Internet of Things (IoT) has drawn important attention in recent years since it has made revolutionary changes in human life. The IoT enables the exchange of information or data in a wide variety of applications such as smart buildings, smart health, smart transport, and so on. As billions of connected things communicate with each other and can interchange sensitive information that may be revealed. Hence, strengthening IoT’s security and preserving users’ privacy is a crucial challenge. The aim of this paper is to provide a comprehensive study of the IoT security. Several IoT security attacks are examined and a taxonomy of the security requirements based on the attacks purposes is proposed. Furthermore, recent security solutions are described and classified based on their application area. Ultimately, open research directions and security challenges are discussed.

Due to the growth of e-commerce, most of the banking transactions are made on the online platform and all these transactions are made on the websites provided by the merchant or the payable apps and because of this the vulnerability of attacks has increased and there are also chances of using fraudulent websites and apps by the attackers though there are many high-security algorithms are been used for safeguarding against vulnerabilities. The way of judging the relation of trust on the online platform has become a major issue, so a proper trust model also needs to be maintained. In this paper, we reviewed various security algorithms which involve cryptographic algorithms, machine learning, anonymization, and masking techniques, blockchain, distributed networks, and many more to provide integrity, privacy, reliability, authentication, security, and risk-less e-commerce platform.

This study explored the relationship between syntactic complexity and rhetorical functions and the relationship between syntactic complexity and level of move/step realization in learner-generated research paper introductions. We created a corpus of 79 introductions written by undergraduate L2 students at intermediate to high-intermediate levels. We annotated the introductions for moves and steps, measured their syntactic complexity at the global, clausal, and phrasal levels, and rated their level of move/step realization across four levels (no, low, intermediate, and high). We conducted one-way MANOVA, one-way ANOVA, Pearson correlation, and stepwise multiple linear regression analyses. We found sentences realizing Reviewing items of previous research function to be significantly longer than other steps in Move1 and to contain significantly more clausal and phrasal complexity features. Sentences performing Claiming centrality function also demonstrated significantly more phrasal complexity features as measured by complex nominals per clause. We also found a higher level of phrasal complexity in introductions with a higher level of move/step realization, which can be attributed to introductions including Step1 and Step3, rather than containing all steps. Our findings imply that there is value in developing explicit instructions on how to use complex structures in performing rhetorical steps in research paper introductions. © 2021 Elsevier Ltd

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

Contains fulltext : 237435.pdf (Publisher’s version ) (Open Access) Objective: We evaluated reporting completeness and transparency in randomised controlled trials (RCTs) conducted using administrative data based on 2021 CONSORT Extension for Trials Conducted Using Cohorts and Routinely Collected Data (CONSORT-ROUTINE) criteria. Study Design and Setting: MEDLINE and the Cochrane Methodology Register were searched (2011 and 2018). Eligible RCTs used administrative databases for identifying eligible participants or collecting outcomes. We evaluated reporting based on CONSORT-ROUTINE, which modified eight items from CONSORT 2010 and added five new items. Results: Of 33 included trials (76% used administrative databases for outcomes, 3% for identifying participants, 21% both), most were conducted in the United States (55%), Canada (18%), or the United Kingdom (12%). Of eight items modified in the extension; six were adequately reported in a majority (>50%) of trials. For the CONSORT-ROUTINE modification portion of those items, three items were reported adequately in >50% of trials, two in

These data were used to build an object detection model to locate Relict Charcoal Hearths (RCH) as described in the paper “When Computers Dream of Charcoal: Using Deep Learning, Open Tools and Open Data to Identify Relict Charcoal Hearths in and around State Game Lands in Pennsylvania” [1]. This is the first grouping of data for the paper above. The second grouping is also available in this journal, see “Object detection model, image data and results from the “When Computers Dream of Charcoal: Using Deep Learning, Open Tools and Open Data to Identify Relict Charcoal Hearths in and around State Game Lands in Pennsylvania” paper”. These files consist of georeferenced Digital Elevation Model, Hillshade and Slope files derived from LiDAR for the State Game Lands (SGL). Included is a Shapefile and GeoJSON of State Game Land borders as well as the program used for downloading the LiDAR files. These data are stored on Zenodo.org .

This companion paper is to support the replication of paper "Campus3D: A Photogrammetry Point Cloud Benchmark for Outdoor Scene Hierarchical Understanding", which was presented at ACM Multimedia 2020. The supported paper's main purpose was to provide a photogrammetry point cloud-based dataset with hierarchical multilabels to facilitate the area of 3D deep learning. Based on this provided dataset and source code, in this work, we build a complete package to reimplement the proposed methods and experiments (i.e., the hierarchical learning framework and the benchmarks of the hierarchical semantic segmentation task). Specifically, this paper contains the technical details of the package, including file structure, dataset preparation, installation package, and the conduction of the experiment. We also present the replicated experiment results and indicate our contributions to the original implementation.

In this paper we reproduce experimental results presented in our earlier work titled "Describing Subjective Experiment Consistency by $p$-Value P-P Plot" that was presented in the course of the 28th ACM International Conference on Multimedia. The paper aims at verifying the soundness of our prior results and helping others understand our software framework. We present artifacts that help reproduce tables, figures and all the data derived from raw subjective responses that were included in our earlier work. Using the artifacts we show that our results are reproducible. We invite everyone to use our software framework for subjective responses analyses going beyond reproducibility efforts., Comment: Please refer to the original publication: https://dl.acm.org/doi/10.1145/3474085.3477935 Related paper: https://dl.acm.org/doi/abs/10.1145/3394171.3413749 or arXiv:2009.13372

Peran teknologi informasi bagi perusahaan mempunyai peranan penting dan dapat menjadi pusat strategi bisnis untuk memperoleh keunggulan bersaing. Saat ini teknologi informasi sudah menjadi kebutuhan dasar bagi setiap perusahaan. Perusahaan yang ingin dikenal secara luas maupun perusahaan yang ingin menjaga hubungan dengan pelanggannya perlu membuat situs/website yang berisi informasi profil perusahaan maupun jasa/produk yang diberikan. Setiap website pasti memiliki sebuah user interface yang berbeda-beda. Klinik Sehat sama seperti klinik pada umumnya yang memberikan pelayanan yang efektif dan efisien. Untuk meningkatkan pelayanan klinik, pihak klinik ingin membuat website yang dapat digunakan pengguna untuk mudah melihat aktifitas yang sedang berlangsung di klinik. Dengan membuat website klinik, tampilan antarmuka (interface) berperan penting dalam pembuatan website. Interface merupakan hal yang di lihat pertama kali pada saat pengguna membuka website Klinik Sehat. Interface menjadi patokan. Untuk membuat interface yang bersifat user friendly pihak kinik membuat interface dengan metode paper prototype. Paper prototype dapat membantu membuat interface pada awal pengembangannya. Hasil yang di dapat pada paper ini adalah metode paper prototype cocok digunakan untuk membuat tampilan user interface pada website seperti Klinik Sehat, tampilan user interface yang user friendly bagi para pengguna website, Pengguna dapat melakukan ujicoba antarmuka dengan aksi-aksi yang nyata dan juga dapat menentukan sendiri aksi atau tugas apa saja yang bisa dipahami dan dilakukan ketika menggunakan aplikasi/website tersebut secara intuitif.

Due to the increasing size of s (s), their design and optimization phases (i.e., ) grow increasingly complex. At design time, a large design space needs to be explored to find an implementation that fulfills all specifications and then optimizes metrics like energy, area, delay, reliability, etc. At run time, a large configuration space needs to be searched to find the best set of parameters (e.g., voltage/frequency) to further optimize the system. Both spaces are infeasible for exhaustive search typically leading to heuristic optimization algorithms that find some trade-off between design quality and computational overhead. ML can build powerful models that have successfully been employed in related domains. In this survey, we categorize how () may be used and is used for design-time and run-time optimization and exploration strategies of s. A meta-study of published techniques unveils areas in that are well-explored and underexplored with, as well as trends in the employed algorithms. We present a comprehensive categorization and summary of the state of the art on for. Finally, we summarize remaining challenges and promising open research directions.

Paper-based analytical devices (PADs) employing colorimetric detection and smartphone images have gained wider acceptance in a variety of measurement applications. The PADs are primarily meant to be used in field settings where assay and imaging conditions greatly vary resulting in less accurate results. Recently, machine learning (ML) assisted models have been used in image analysis. We evaluated a combinations of four ML models - logistic regression, support vector machine, random forest, and artificial neural network, and three image color spaces - RGB, HSV, and LAB for their ability to accurately predict analyte concentrations. We used images of PADs taken at varying lighting conditions, with different cameras, and users for food color and enzyme inhibition assays to create training and test datasets. Prediction accuracy was higher for food color than enzyme inhibition assays in most of the ML model and colorspace combinations. All models better predicted coarse level classification than fine grained concentration labels. ML models using sample color along with a reference color increased the models’ ability in predicting the result in which the reference color may have partially factored out the variation in ambient assay and imaging conditions. The best concentration label prediction accuracy obtained for food color was 0.966 when using ANN model and LAB colorspace. The accuracy for enzyme inhibition assay was 0.908 when using SVM model and LAB colorspace. Appropriate model and colorspace combinations can be useful to analyze large numbers of samples on PADs as a powerful low-cost quick field-testing tool.

Attention to the environment and its problems has undergone unprecedented growth in recent years [...]

This special section presents an updated version of the paper that won the first prize award in the ITU (International Telecommunication Union) Kaleidoscope conference (K-2020).

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.

Bacteria identification has predominantly been conducted using specific bioreceptors such as antibodies or nucleic acid sequences. This approach may be inappropriate for environmental monitoring when the user does not know the target bacterial species and for screening complex water samples with many unknown bacterial species. In this work, we investigate the supervised machine learning of the bacteria-particle aggregation pattern induced by the peptide sets identified from the biofilm-bacteria interface. Each peptide is covalently conjugated to polystyrene particles and loaded together with bacterial suspensions onto paper microfluidic chips. Each peptide interacts with bacterial species to a different extent, leading to varying sizes of particle aggregation. This aggregation changes the surface tension and viscosity of the liquid flowing through the paper pores, altering the flow velocity at different extents. A smartphone camera captures this flow velocity without being affected by ambient and environmental conditions, towards a low-cost, rapid, and field-ready assay. A collection of such flow velocity data generates a unique fingerprinting profile for each bacterial species. Support vector machine is utilized to classify the species. At optimized conditions, the training model can predict the species at 93.3% accuracy out of five bacteria: Escherichia coli, Staphylococcus aureus, Salmonella Typhimurium, Enterococcus faecium, and Pseudomonas aeruginosa. Flow rates are monitored for less than 6 s and the sample-to-answer assay time is less than 10 min. The demonstrated method can open a new way of analyzing complex biological and environmental samples in a biomimetic manner with machine learning classification.

Motion information has been widely exploited for group activity recognition in sports video. However, in order to model and extract the various motion information between the adjacent frames, existing algorithms only use the coarse video‐level labels as supervision cues. This may lead to the ambiguity of extracted features and the omission of changing rules of motion patterns that are also important sports video recognition. In this paper, a latent label mining strategy for group activity recognition in basketball videos is proposed. The authors' novel strategy allows them to obtain the latent labels set for marking different frames in an unsupervised way, and build the frame‐level and video‐level representations with two separate levels of supervision signal. Firstly, the latent labels of motion patterns are digged using the unsupervised hierarchical clustering technique. The generated latent labels are then taken as the frame‐level supervision signal to train a deep CNN for the frame‐level features extraction. Lastly, the frame‐level features are fed into an LSTM network to build the spatio‐temporal representation for group activity recognition. Experimental results on the public NCAA dataset demonstrate that the proposed algorithm achieves state‐of‐the‐art performance.

The electronic document management system is one of the most popular products for implementation at various enterprises in various industries, ranging from heavy industry to state organizations and federal authorities. Document flow in many companies is carried out on paper, and this, in turn, causes great difficulties in processing, storing and executing documents. Paper archives occupy hundreds of square meters of storage space, and if necessary, it is very difficult to find the right document among a large amount of waste paper. In this regard, many companies begin to review their activities and move away from paper document management to electronic

Background Clinical guidelines on infection control strategies in healthcare workers (HCWs) play an important role in protecting them during the severe acute respiratory syndrome coronavirus 2 pandemic. Poorly constructed guidelines that are incomprehensive and/or ambiguous may compromise HCWs’ safety. Objective The objective of this study was to develop and validate a tool to appraise guidelines on infection control strategies in HCWs based on the guidelines published early in the coronavirus disease 2019 pandemic. Design, setting, and outcomes A three-stage, web-based, Delphi consensus-building process among a panel of diverse HCWs and healthcare managers was performed. The tool was validated by appraising 40 international, specialty-specific, and procedure-specific guidelines along with national guidelines from countries with a wide range of gross national income. Results Overall consensus (≥75%) was reached at the end of three rounds for all six domains included in the tool. The Delphi panel recommended an ideal infection control guideline should encompass six domains: general characteristics (domain 1), engineering recommendations (domain 2), personal protective equipment (PPE) use (domain 3), and administrative aspects (domain 4-6) of infection control. The appraisal tool performed well across the six domains, and the inter-rater agreement was excellent for the 40 guidelines. All included guidelines performed relatively better in domains 1–3 than in domains 4–6, and this was more evident in guidelines originating from lower income countries. Conclusion The guideline appraisal tool was robust and easy to use. Engineering recommendations aspects of infection control, administrative measures that promote optimal PPE use, and HCW wellbeing were generally lacking in assessed guidelines. This tool may enable health systems to adopt high-quality HCW infection control guidelines during the severe acute respiratory syndrome coronavirus 2 pandemic and may also provide a framework for future guideline development.

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.

Texts are not monolithic entities but rather coherent collections of micro illocutionary acts which help to convey a unitary message of content and purpose. Identifying such text segments is challenging because they require a fine-grained level of analysis even within a single sentence. At the same time, accessing them facilitates the analysis of the communicative functions of a text as well as the identification of relevant information. We propose an empirical framework for modelling micro illocutionary acts at clause level, that we call content types, grounded on linguistic theories of text types, in particular on the framework proposed by Werlich in 1976. We make available a newly annotated corpus of 279 documents (for a total of more than 180,000 tokens) belonging to different genres and temporal periods, based on a dedicated annotation scheme. We obtain an average Cohen’s kappa of 0.89 at token level. We achieve an average F1 score of 74.99% on the automatic classification of content types using a bi-LSTM model. Similar results are obtained on contemporary and historical documents, while performances on genres are more varied. This work promotes a discourse-oriented approach to information extraction and cross-fertilisation across disciplines through a computationally-aided linguistic analysis.

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.

The title molecule, [Sn(C8H3F6)4], lies on a twofold rotation axis with the SnIV ion in a distorted tetrahedral coordination environment. Both –CF3 groups attached to one of the unique benzene rings are disordered over two sets of sites, with the ratios of refined occupancies being 0.719 (14):0.281 (14) and 0.63 (5):0.37 (5).

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.

During the outbreak of emerging infectious diseases, media coverage and medical resource play important roles in affecting the disease transmission. To investigate the effects of the saturation of media coverage and limited medical resources, we proposed a mathematical model with extra compartment of media coverage and two nonlinear functions. We theoretically and numerically investigate the dynamics of the proposed model. Given great difficulties caused by high nonlinearity in theoretical analysis, we separately considered subsystems with only nonlinear recovery or with only saturated media impact. For the model with only nonlinear recovery, we theoretically showed that backward bifurcation can occur and multiple equilibria may coexist under certain conditions in this case. Numerical simulations reveal the rich dynamic behaviors, including forward-backward bifurcation, Hopf bifurcation, saddle-node bifurcation, homoclinic bifurcation and unstable limit cycle. So the limitation of medical resources induces rich dynamics and causes much difficulties in eliminating the infectious diseases. We then investigated the dynamics of the system with only saturated media impact and concluded that saturated media impact hardly induces the complicated dynamics. Further, we parameterized the proposed model on the basis of the COVID-19 case data in mainland China and data related to news items, and estimated the basic reproduction number to be 2.86. Sensitivity analyses were carried out to quantify the relative importance of parameters in determining the cumulative number of infected individuals at the end of the first month of the outbreak. Combining with numerical analyses, we suggested that providing adequate medical resources and improving media response to infection or individuals' response to mass media may reduce the cumulative number of the infected individuals, which mitigates the transmission dynamics during the early stage of the COVID-19 pandemic.

Background Knowledge translation and dissemination are some of the main challenges that affect evidence-based medicine. Web 2.0 platforms promote the sharing and collaborative development of content. Executable knowledge tools, such as order sets, are a knowledge translation tool whose localization is critical to its effectiveness but a challenge for organizations to develop independently. Objective This paper describes a Web 2.0 resource, referred to as the collaborative network (TCN), for order set development designed to share executable knowledge (order sets). This paper also analyzes the scope of its use, describes its use through network analysis, and examines the provision and use of order sets in the platform by organizational size. Methods Data were collected from Think Research’s TxConnect platform. We measured interorganization sharing across Canadian hospitals using descriptive statistics. A weighted chi-square analysis was used to evaluate institutional size to share volumes based on institution size, with post hoc Cramer V score to measure the strength of association. Results TCN consisted of 12,495 order sets across 683 diagnoses or processes. Between January 2010 and March 2015, a total of 131 health care organizations representing 360 hospitals in Canada downloaded order sets 105,496 times. Order sets related to acute coronary syndrome, analgesia, and venous thromboembolism were most commonly shared. COVID-19 order sets were among the most actively shared, adjusting for order set lifetime. A weighted chi-square analysis showed nonrandom downloading behavior (P Conclusions In this paper, we have described and analyzed a Web 2.0 platform for the sharing of order set content with significant network activity. The robust use of TCN to access customized order sets reflects its value as a resource for health care organizations when they develop or update their own order sets.

Background: A clinical decision support system (CDSS) has been designed to predict the outcome (overall survival) by extracting and analyzing information from routine clinical activity as a complement to clinical guidelines in lung cancer patients. Materials and methods: Prospective multicenter data from 543 consecutive (2013–2017) lung cancer patients with 1167 variables were used for development of the CDSS. Data Mining analyses were based on the XGBoost and Generalized Linear Models algorithms. The predictions from guidelines and the CDSS proposed were compared. Results: Overall, the highest (> 0.90) areas under the receiver-operating characteristics curve AUCs for predicting survival were obtained for small cell lung cancer patients. The AUCs for predicting survival using basic items included in the guidelines were mostly below 0.70 while those obtained using the CDSS were mostly above 0.70. The vast majority of comparisons between the guideline and CDSS AUCs were statistically significant (p < 0.05). For instance, using the guidelines, the AUC for predicting survival was 0.60 while the predictive power of the CDSS enhanced the AUC up to 0.84 (p = 0.0009). In terms of histology, there was only a statistically significant difference when comparing the AUCs of small cell lung cancer patients (0.96) and all lung cancer patients with longer (≥ 18 months) follow up (0.80; p < 0.001). Conclusions: The CDSS successfully showed potential for enhancing prediction of survival. The CDSS could assist physicians in formulating evidence-based management advice in patients with lung cancer, guiding an individualized discussion according to prognosis. Instituto de Salud Carlos III PI16/02104 Junta de Andalucía PIN-0476-2017 Ministerio de Economía y Competitividad FPAP13-1E-2429

The cannabis plant is essentially a variety of the Cannabis Sativa L. plant. It is used in the textile, energy, automotive and cosmetics. The use of oil derived from hemp seeds has become widespread in cosmetics. Hemp seed oil does not contain Δ9-tetrahydrocannabinol (Δ9-THC) and it is used in the production of food, biodiesel and polymers as well as cosmetics. In this study, different concentrations of hemp seed oil were used in cream and soap formulations, which are among the cosmetic products, and effect on skin hydration, sebum and transepidermal water loss (TEWL) on the skin was investigated. At the same time, the foaming test was applied to soaps containing different concentrations of hemp seed oil to see effects of soap foam performance. To analyse these, a rinse-off and leave-on product were selected. In soap formulations, there is positive effect on skin hydration and TEWL with sebum decrease. The most important change in cream formulations with respect to bar soap formulations is the increases in sebum. The effects of hemp seed oil on soap foam performance were examined. As a result of the study, its effect on the foam of the soap base which is used in this study is positive.

A number of the people who have recovered from the acute effects of COVID-19 are facing long term sequelae from the infection. As the COVID-19 pandemic is still evolving, so is knowledge of the long-term effects of the virus on patients who still experience symptoms. Clearly, news media play a crucial role in distributing information and this distribution of information can, in turn, influence the actions of the public. The purpose of this study was to describe the content of news coverage of COVID-19 long haul symptoms currently posted on the internet. This study utilized Google News, a news aggregator service, and included the first 100 English language pieces of news. Video content and news article content were coded in depth for information on COVID-19 long haul symptoms. A total of 41% of news reports mentioned the length of time that the COVID-19 related symptoms persist. The length of time was reported to range from 1 month to more than 1 year. The symptom most commonly mentioned was tiredness or fatigue (74%), followed by difficulty breathing or shortness of breath (62 cases; 62%), and difficulty thinking or concentrating (50 cases; 50%). Other symptoms were mentioned less frequently. There were no statistically significant differences in any of the content including having video, written news reports, or both video and written news reports by source of the news reports based on consumer, professional, or television or internet-based news (p = .14). More complete coverage by online news media of the long-term effects of COVID-19 enhances public awareness of the post-acute syndromes, augments health providers' awareness of the range of chronic COVID-19 effects and the possibility of a second infection, increases the probability of patients' seeking and obtaining the proper care for their symptoms, and contributes to preventive actions for enhancing public health.

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.

Chatbots are increasingly becoming important gateways to digital services and information—taken up within domains such as customer service, health, education, and work support. However, there is only limited knowledge concerning the impact of chatbots at the individual, group, and societal level. Furthermore, a number of challenges remain to be resolved before the potential of chatbots can be fully realized. In response, chatbots have emerged as a substantial research area in recent years. To help advance knowledge in this emerging research area, we propose a research agenda in the form of future directions and challenges to be addressed by chatbot research. This proposal consolidates years of discussions at the CONVERSATIONS workshop series on chatbot research. Following a deliberative research analysis process among the workshop participants, we explore future directions within six topics of interest: (a) users and implications, (b) user experience and design, (c) frameworks and platforms, (d) chatbots for collaboration, (e) democratizing chatbots, and (f) ethics and privacy. For each of these topics, we provide a brief overview of the state of the art, discuss key research challenges, and suggest promising directions for future research. The six topics are detailed with a 5-year perspective in mind and are to be considered items of an interdisciplinary research agenda produced collaboratively by avid researchers in the field.

We report the results of a novel protocol for running online experiments using a combination of an online experimental platform in parallel with web-conferencing software in two formats—with and without subject webcams—to improve subjects’ attention and engagement. We compare the results between our online sessions with the offline (lab) sessions of the same experiment. We find that both online formats lead to comparable subject characteristics and performance as the offline (lab) experiment. However, the webcam-on protocol has less noisy data, and hence better statistical power, than the protocol without a webcam. The webcam-on protocol can detect reasonable effect sizes with a comparable sample size as in the offline (lab) protocol. Supplementary Information The online version contains supplementary material available at 10.1007/s40881-021-00112-w.

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.

Methods to quantify biological aging are emerging as new measurement tools for epidemiology and population science and have been proposed as surrogate measures for healthy lifespan extension in geroscience clinical trials. Publicly available software packages to compute biological aging measurements from DNA methylation data have accelerated dissemination of these measures and generated rapid gains in knowledge about how different measures perform in a range of datasets. Biological age measures derived from blood chemistry data were introduced at the same time as the DNA methylation measures and, in multiple studies, demonstrate superior performance to these measures in prediction of healthy lifespan. However, their dissemination has been slow by comparison, resulting in a significant gap in knowledge. We developed a software package to help address this knowledge gap. The BioAge R package, available for download at GitHub (http://github.com/dayoonkwon/BioAge), implements three published methods to quantify biological aging based on analysis of chronological age and mortality risk: Klemera-Doubal biological age, PhenoAge, and homeostatic dysregulation. The package allows users to parametrize measurement algorithms using custom sets of biomarkers, to compare the resulting measurements to published versions of the Klemera-Doubal method and PhenoAge algorithms, and to score the measurements in new datasets. We applied BioAge to safety lab data from the CALERIE™ randomized controlled trial, the first-ever human trial of long-term calorie restriction in healthy, non-obese adults, to test effects of intervention on biological aging. Results contribute evidence that CALERIE intervention slowed biological aging. BioAge is a toolkit to facilitate measurement of biological age for geroscience. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11357-021-00480-5.

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.

It is widely thought that individuals age at different rates. A method that measures “physiological age” or physiological aging rate independent of chronological age could therefore help elucidate mechanisms of aging and inform an individual’s risk of morbidity and mortality. Here we present machine learning frameworks for inferring individual physiological age from a broad range of biochemical and physiological traits including blood phenotypes (e.g., high-density lipoprotein), cardiovascular functions (e.g., pulse wave velocity) and psychological traits (e.g., neuroticism) as main groups in two population cohorts SardiNIA (~6,100 participants) and InCHIANTI (~1,400 participants). The inferred physiological age was highly correlated with chronological age (R2 > 0.8). We further defined an individual’s physiological aging rate (PAR) as the ratio of the predicted physiological age to the chronological age. Notably, PAR was a significant predictor of survival, indicating an effect of aging rate on mortality. Our trait-based PAR was correlated with DNA methylation-based epigenetic aging score (r = 0.6), suggesting that both scores capture a common aging process. PAR was also substantially heritable (h2~0.3), and a subsequent genome-wide association study of PAR identified significant associations with two genetic loci, one of which is implicated in telomerase activity. Our findings support PAR as a proxy for an underlying whole-body aging mechanism. PAR may thus be useful to evaluate the efficacy of treatments that target aging-related deficits and controllable epidemiological factors.

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.

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.