bluuebunny/crossref_metadata_2025 huggingface dataset:
Delineation of electrocardiogram morphologies by using discrete wavelet transforms
Authors: Darmawahyuni Annisa , Nurmaini Siti , Habibie Supriansyah Hanif , Rizki Fauzi Muhammad Irham , Naufal Rachmatullah Muhammad , Firdaus Firdaus , Tutuko Bambang
Published: April 2021

The accuracy of electrocardiogram (ECG) delineation can affect the precise diagnose for cardiac disorders interpretation. Some nonideal ECG presentation can make a false decision in precision medicine. Besides, the physiological variation of heart rate and different characteristics of the different ECG waves in terms of shape, frequency, amplitude, and duration is also affected. This paper proposes a discrete wavelet transform (DWT), non-stationary signal analysis for noise removal, and onset-offset of PQRST feature extraction. A well-known database from Physionet: QT database (QTDB) is used to validate the DWT function for detecting the onset and offset of P-wave, QRS-complex, and T-wave localization. From the results, P-peak detection gets the highest result that achieves 2.19 and 13.62 milliseconds of mean error and standard deviation, respectively. In contrast, Toff has obtained the highest error value due to differences in the T-wave morphology. It can be affected by inverted or biphasic T-waves and others.
IoT and transparent solar cell based automated green house monitoring system for tomato plant cultivation
Authors: Rama Denny Yus , Permata Endi , Trenggono Adhitya , Gustiono Vaka
Published: April 2021

This study aimed to develop and test the feasibility of a smart greenhouse prototype media that is used as a planting medium with an automatic watering system. The method in this study was research and development using the waterfall model. In order to test the feasibility, the prototype was validated with material expert validators, media expert, and farmers. The questionnaire instrument was compiled based on Walker and Hess instrument. The results of the research found are as follows: the results of feasibility research by media experts has an average score of 4.35 with the category "very feasible", assessment by experts the material has an average score of 4.4 with the category "very feasible", and the assessment of the user has an average score of 4.06 with "feasible". The purposed controlled system of smart greenhouse and as a media for farmers was validated. Our results demonstrated that the smart greenhouse is suitable media to help farmers cultivating the tomatoes plant.
Evaluation comparison of wave amount measurement results in brass-plated tire steel cord using RMSE and cosine similarity
Authors: Lia Hananto April , Sulaiman Sarina , Widiyanto Sigit , Yuniar Rahman Aviv
Published: April 2021

In the production process, quality checking is very important, one of which is on the wire. In the process of making brass-coated steel tire straps sometimes produce quality goods not in accordance with the desired standard values. Checks that are carried out manually have low efficiency and quite high errors occur. So it is necessary to check by measuring the wavelength on the brass plated steel cord automatically. In this study, used 3 automatic measurement methods using 2 evaluations, namely RMSE and Cosine Similarity. The results showed the best measurement using RMSE with method 2. Whereas the worst method uses RMSE with method 1. The smallest RMSE value is 0.0098 and the largest RMSE is 0.0966. The lowest Cosine Similarity value is 0.1253, while the highest Cosine Similarity value is 0.2079.
Efficient intelligent system for diagnosis pneumonia (SARS-COVID19) in X-Ray images empowered with initial clustering
Authors: Mohamed Ali Salam Saad , Alsaeedi Ali Hakem , Al-Shammary Dhiah , Alsaeedi Hassan Hakem , Abid Hadeel Wajeeh
Published: April 2021

This paper proposes efficient models to help diagnose respiratory (SARS-COVID19) infections by developing new data descriptors for standard machine learning algorithms using X-Ray images. As COVID-19 is a significantly serious respiratory infection that might lead to losing life, artificial intelligence plays a main role through machine learning algorithms in developing new potential data classification. Data clustering by K-Means is applied in the proposed system advanced to the training process to cluster input records into two clusters with high harmony. Principle Component Analysis PCA, histogram of orientated gradients (HOG) and hybrid PCA and HOG are developed as potential data descriptors. The wrapper model is proposed for detecting the optimal features and applied on both clusters individually. This paper proposes new preprocessed X-Ray images for dataset featurization by PCA and HOG to effectively extract X-Ray image features. The proposed systems have potentially empowered machine learning algorithms to diagnose Pneumonia (SARS-COVID19) with accuracy up to %97.
Economic technology analysis of LTE advanced pro dual spectrum licensed and unlicensed access using discounted cash flow methods
Authors: Budiyanto Setiyo , Al Hakim Erman , Rahayu Fajar
Published: April 2021

Since implementing the long term evolution (LTE) technology, the surge in data service traffic has increased, causing an increase in demand spectrum, which has resulted in gaps in capacity requirements. Wireless service providers can respond to LTE technology updates. With LTE advanced pro technology that utilizes unlicensed spectrum technology can provide solutions to increase capacity and throughput. In this study, LTE advanced pro planning by capacity method to find the number of eNodeB and using the discounted cash flow method to analyze the feasibility of the costs to be invested in the implementation of the LTE. The results of the four simulated scenarios concluded that the number of eNodeB from the IV scenario with 20 MHz bandwidth at 1800 MHz frequency and 20 MHz bandwidth at 5 GHz frequency amounted to 23 sites, with a positive NPV value of $ 271,936.96, IRR of 14.91%, and for payback period occurred in the 3rd year. Thus the fourth scenario is feasible to be implemented.
Attitude on intention to use e-government in Indonesia
Authors: Afrizal Dedy , Wallang MUslimin
Published: April 2021

The application of information and communication technologies in Indonesia continues to be developed as the government becomes more serious in improving services to its citizen. However, there are still some obstacles to using the service. The purpose of this paper to present a framework improving e-government services to its citizen. The paper opted for using a comprehensive review of the unified theory of acceptance and use of technology (UTAUT). This paper offers ideas to see intention to the community in using e-government, by using the modified UTAUT model where the main construct performance expectancy (PE), effort expectancy (EE), social influence (SI), facilitating conditions (FC) is an important factor. Moderators such as gender, age, experience and voluntariness of use were excluded and using attitude as a mediator. The findings showed that UTAUT’s construct such as performance expectancy, effort expectancy, social influence, facilitating conditions is an important factor appropriate for seeing intention to citizen in using e-government and 9 hypotheses offered in the model are believed to get new findings in the future and increase the development of the UTAUT model and be able to provide concept ideas that are made in seeing the intentions of e-government users.
The trend malware source of IoT network
Authors: Susanto Susanto , Syamsul Arifin M. Agus , Stiawan Deris , Yazid Idris Mohd. , Budiarto Rahmat
Published: April 2021

Malware may disrupt the internet of thing (IoT) system/network when it resides in the network, or even harm the network operation. Therefore, malware detection in the IoT system/network becomes an important issue. Research works related to the development of IoT malware detection have been carried out with various methods and algorithms to increase detection accuracy. The majority of papers on malware literature studies discuss mobile networks, and very few consider malware on IoT networks. This paper attempts to identify problems and issues in IoT malware detection presents an analysis of each step in the malware detection as well as provides alternative taxonomy of literature related to IoT malware detection. The focuses of the discussions include malware repository dataset, feature extraction methods, the detection method itself, and the output of each conducted research. Furthermore, a comparison of malware classification approaches accuracy used by researchers in detecting malware in IoT is presented.
Measuring information security policy compliance: content validity of questionnaire
Authors: Angraini Angraini , Alinda Alias Rose , Okfalisa Okfalisa
Published: April 2021

Instruments used to measure compliance with information security policies have been developed by many researchers before, but only a few have conducted validity tests per item, especially for variables selected based on qualitative research. This study aims to validate the questionnaire will be used to measure user compliance with policies of information security. This study began by designing a questionnaire and conducting content validation using content ratio validation (CVR) and content index validation (CVI). As many as eight experts from the university assessed the items given. The results of 72 items submitted a questionnaire, as many as 22 items eliminated, and only 50 items that have CVR and CVI values above 0.75. Also, Kappa statistical calculations show that items have excellent reliability among assessors at the item level. This study revealed that this instrument had obtained an appropriate level of validity to measure compliance with information security policies. 
Pushing towards ehealth for iraqi hypertensives: an integrated class association rules into SECI model
Authors: Aljuboori Ahmed , Tawfeeq Lubab Ahmed , Al-Karawi Khamis A.
Published: April 2021

This paper highlights the barriers that have led to a delay in the implementation of E-Health services in Iraq. A new framework is proposed to improve the E-Health sector using a SECI model which describes how explicit and tacit knowledge is generated, transferred, and recreated in organizations through main stages (socialization, externalization, combination and internalization). Class association rules (CARs) is integrated to mine the SECI model by extracting related rules which correspond to the medical advice. The proposed framework (SECICAR) can be done through a web portal to assemble healthcare professionals, patients in one environment. SECICAR will be applied to the hypertension community to show that disease if left untreated, frequently leads to serious illnesses such as heart disease. The SECICAR aims to facilitate the dissemination of tacit knowledge, which is explicit to hypertensives, in the form of strategies, guidelines and best practices. The validation of the SECICAR results displays satisfactory accuracy and reliability. Heuristic evaluation was used to test the web portal, the participants stating that there were no major issues regarding its usability.
Air temperature prediction using different machine learning models
Authors: Adnan Rana Muhammad , Liang Zhongmin , Kuriqi Alban , Kisi Ozgur , Malik Anurag , Li Binquan , Mortazavizadeh Fatemehsadat
Published: April 2021

Air temperature is an essential climatic component particularly in water resources management and other agro-hydrological/meteorological activities planning This paper examines the prediction capability of three machine learning models, least square support vector machine (LSSVM), group method and data handling neural network (GMDHNN) and classification and regression trees (CART) in air temperature forecasting using monthly temperature data of Astore and Gilgit climatic stations of Pakistan. The prediction capability of three machine learning models is evaluated using different time lags input combinations with help of root mean square error (RMSE), the mean absolute error (MAE) and coefficient of determination (R2).statistical indicators. The obtained results indicated that the LSSVM model is more accurate in temperature forecasting than GMDHNN and CART models. LSSVM significantly decreases the mean RMSE of the GMHNN and CART models by 1.47-3.12% and 20.01-25.12% for the Chakdara and Kalam Stations, respectively.
Analysis of the performance of grounding grids buried in heterogeneous soil under impulse current
Authors: Djaborebbi Amina , Zegnini Boubakeur , Mahi Djillali
Published: April 2021

The present paper is devoted to analyzing the transient behaviour of simple grounding grids subjected to impulse lightning current. The transmission line method (TLM) involving mutual coupling between conductors will be used. The transient behaviour of grounding grids buried in homogeneous and in heterogeneous soil is going to be evaluated into a complete time domain solution. Different simulations carried out altering, the influence of the grid dimensions, the kind of the ground and the current injection point on the grid voltage and impedance will be presented. Simulation results will be shown for two extreme cases: in the first case the current is in the center of the grid and in the second one it is injected in one corner of the two configurations of grids. The obtained results show that the grid 1x1 gives the lowest transient potential when the injection point is in lower resistivity side, and the grid 2x2 presents better behavior when the current is injected at center point. It is obvious that the suggested simulations are in a good agreement, with corresponding results of other researchers.
Improved Lagrangian relaxation generation decision-support in presence of electric vehicles
Authors: Zeynal Hossein , Zakaria Zuhaina , Kor Ahmad
Published: April 2021

Decision making strategies for resources available in macro/micro scales have long been a critical argument. Among existing methods to address such a mixed-binary optimization model, Lagrangian relaxation (LR) found universal acceptance by many utilities, offering a fast and accurate answer. This paper aims at retrofitting the solution way of LR algorithm by dint of meta-heuristic cuckoo search algorithm (CSA). When integrating CSA into LR mechanism, a tighter duality gap is catered, representing more accurate feasible solution. The key performance of CSA exhibits a head start over other classical methods such as gradient search (GS) and Newton Raphson (NR) when dealt with the relative duality gap closure in LR procedure. Further, electric vehicles (EV) with its associated hard constraints are encompassed into model to imperiling the proposed CSA-LR if encountered with nonlinear fluctuation of duality gap. Simulation results show that the proposed CSA-LR model outperforms the solution quality with/without EV as compared with conventional NR-LR method.
Real-time FPGA implementation of concatenated AES and IDEA cryptography system
Authors: M. Hassan Sara , G. Hamza Gihan.
Published: April 2021

The data encryption is one of the most critical issues in the communication system design. Nowadays, many encryption algorithms are being updated to keep pace with the remarkable progress in the communication field. The advanced encryption standard (AES) is a common algorithm that has proved its efficacy. The main drawback of AES is that it uses too simple algebraic structures, since every block is always encrypted in the same way that makes the hacking process possible if the hacker captures the key and the uses S-Box in the input stage. This especially applies to the unwired communication systems where chances of hacking exceed those found in the wired systems. The paper proposes a security enhancement method that is based on utilizing concatenated AES and international data encryption algorithm (IDEA) algorithms. Upon applying the proposed algorithm, the hacking process becomes a great challenge. The paper incorporates the real-time FPGA implementation of the proposed algorithm in the encryption and the decryption stages. Besides, the paper presents a clear analysis of the system’s performance.
High-Density Lipoprotein Anti-Inflammatory Capacity and Incident Cardiovascular Events
Authors: Jia Congzhuo , Anderson Josephine L.C. , Gruppen Eke G. , Lei Yu , Bakker Stephan J.L. , Dullaart Robin P.F. , Tietge Uwe J.F.
Published: April 2021

Background:

The role of high-density lipoprotein (HDL) function in cardiovascular disease represents an important emerging concept. The present study investigated whether HDL anti-inflammatory capacity is prospectively associated with first cardiovascular events in the general population.

Methods:

HDL anti-inflammatory capacity was determined as its ability to suppress TNFα (tumor necrosis factor α)–induced VCAM-1 (vascular cell adhesion molecule-1) mRNA expression in endothelial cells in vitro (results expressed as achieved percent reduction by individual HDL related to the maximum TNFα effect with no HDL present). In a nested case-control design of the PREVEND (Prevention of Renal and Vascular End Stage Disease) study, 369 cases experiencing a first cardiovascular event (combined end point of death from cardiovascular causes, ischemic heart disease, nonfatal myocardial infarction, and coronary revascularization) during a median of 10.5 years of follow-up were identified and individually matched to 369 controls with respect to age, sex, smoking status, and HDL cholesterol. Baseline samples were available in 340 cases and 340 matched controls.

Results:

HDL anti-inflammatory capacity was not correlated with HDL cholesterol or hsCRP (high-sensitivity C-reactive protein). HDL anti-inflammatory capacity was significantly lower in cases compared with controls (31.6% [15.7–44.2] versus 27.0% [7.4–36.1];
P
<0.001) and was inversely associated with incident CVD in a fully adjusted model (odds ratio [OR] per 1 SD, 0.74 [CI, 0.61–0.90];
P
=0.002). Furthermore, this association was approximately similar with all individual components of the cardiovascular disease end point. The HDL anti-inflammatory was not correlated with cholesterol efflux capacity (
r
=−0.02;
P
>0.05). When combining these 2 HDL function metrics in 1 model, both were significantly and independently associated with incident cardiovascular disease in a fully adjusted model (efflux: OR per 1 SD, 0.74;
P
=0.002; anti-inflammatory capacity: OR per 1 SD, 0.66;
P
<0.001). Adding HDL anti-inflammatory capacity improved risk prediction by the Framingham risk score, with a model likelihood-ratio statistic increase from 10.50 to 20.40 (
P
=0.002).

Conclusions:

The HDL anti-inflammatory capacity, reflecting vascular protection against key steps in atherogenesis, was inversely associated with incident cardiovascular events in a general population cohort, independent of HDL cholesterol and HDL cholesterol efflux capacity. Adding HDL anti-inflammatory capacity to the Framingham risk score improves risk prediction.
“No other name!” The Contribution of Byang H. Kato to the Salvation Debate
Authors: van Veelen Wouter Theodoor
Published: April 2021

This article attempts to investigate the contribution of the African evangelical theologian and church leader Byang H. Kato (1936–1975) to the salvation debate in the early 1970s. Due to his radical standpoint and at times uncompromising tone, Kato’s soteriological proposals have been characterized as a reproduction of western theology. This article aims to demonstrate that, rather than reiterating a specific American or western concept of theology, Kato’s soteriology should be read as a contextual evangelical response to the ongoing theological debates of his time.
On Chenopodium rugosum (Chenopodiaceae), an enigmatic taxon described by Aellen from Siberia
Authors: MOSYAKIN SERGEI L. , ROMASCHENKO KONSTANTIN
Published: April 2021

Chenopodium rugosum was described by Aellen in 1928, based on a specimen collected in Siberia by Arnell and deposited in the US Herbarium. For a long time, this Aellen’s name was forgotten or ignored by the researchers, mainly because of the uncertain identity of that taxon and unavailability of its type. We report here the holotype of C. rugosum recently found in US. The specimen was collected in 1876 by Arnell in Verkhneimbatsk (Turukhanskiy District, Krasnoyarskiy Kray, Russia) at the confluence of the Verkhniy Imbach River and the Yenisei River. Taxonomically the holotype of C. rugosum clearly belongs to the C. album aggregate and morphologically seems to be similar to C. striatiforme, a tetraploid “microspecies” related to C. betaceum. However, C. rugosum might be also a hexaploid close to C. album s. str. From a nomenclatural viewpoint, the name C. rugosum by Aellen is illegitimate, being a later homonym of the long-forgotten earlier name C. rugosum validated by Rafinesque in 1830 for some forms of C. ambrosioides (now recognized in Dysphania). Taxonomic and nomenclatural comments are provided on these names.
Nomenclatural notes in the Pleurothallidinae (Orchidaceae): miscellaneous part II

Authors: KARREMANS ADAM P. , ROJAS-ALVARADO GUSTAVO , BEZERRA-SILVA LUIZ EDUARDO , FLORES-ROJAS JEFFREY , MURILLO-MURILLO JOSE MARTÍN , ROMERO-CECILIANO MARYSOL , SEGURA-BERMÚDEZ OSCAR A.
Published: April 2021

Nomenclatural changes and notes are provided for genera in subtribe Pleurothallidinae (Epidendroideae: Orchidaceae) to comply with the International code of nomenclature for algae, fungi, and plants. The proposed changes include new names and combinations, author citations, spelling and synonymy. Brief notes are also provided.
“Close Enough”: Images of the Failure of the 1990s’ Political Transformation in Poland as Exemplified by Władysław Pasikowski’s “Psy” [Pigs] and Andrzej Żuławski’s “Szamanka” [She-Shaman]
Authors: Szczepanek Tomasz
Published: April 2021

This article problematizes the Polish cinema of the 1990s by analyzing it in terms of the aesthetic of failure. Of crucial importance for that interpretation is the postcolonial perspective. Seen from this perspective, Poland of the political transformation period appears a land of unfulfilled dreams of being-like-the-West. One of the spheres where this is visible is the Polish cinematography of that time.
Disgrace, Weakness, Rubbish? Material Culture of the GDR in Selected German Films After 1990
Authors: Brzezińska-Pająk Marta
Published: April 2021

The article focuses on the material culture of the German Democratic Republic (GDR) as portrayed in selected German films made after 1990 and set in the GDR. The objects that are used in the films serve as a special kind of artefacts, symbolizing the reality of the GDR and defining it as imperfect, below expectations, and inefficient in meeting consumer demand. An important point of reference in the article is the context of post-communist nostalgia, which is a source of interesting symbolic redefinitions.
“Born Out of Crisis, Buried by Catastrophe”: Central Europe as a Project Doomed to Failure
Authors: Parfianowicz Weronika
Published: April 2021

In her paper, the author examines images of Central Europe created in various popular genres (campus novels, quasi-guidebooks, films, essays) as well as interpretations of the Central European myth from countries of the region. The aim is to reflect on two main Central European narratives. One is a vision of retrospective utopia of lost harmonious coexistence of cultures, religions and nations. The other – an image of the “misery of small Central European states”, of a backward region, immersed in never-ending ethnic conflicts. The author seeks to address the question of how these narratives influence the interpretation of the systemic transition process and of contemporary problems that the region is facing.
A Record-Breaking Trans-Atlantic African Dust Plume Associated with Atmospheric Circulation Extremes in June 2020
Authors: Pu Bing , Jin Qinjian
Published: April 2021

High concentrations of dust can affect climate and human health, yet our understanding of extreme dust events is still limited. A record-breaking trans-Atlantic African dust plume occurred during 14–28 June 2020, greatly degrading air quality over large areas of the Caribbean Basin and the United States. Daily PM2.5 concentrations exceeded 50 µg m−3 in several Gulf States, while the air quality index reached unhealthy levels for sensitive groups in more than 11 states. The magnitude and duration of aerosol optical depth over the tropical North Atlantic Ocean were the greatest ever observed during summer over the past 18 years based on satellite retrievals. This extreme trans-Atlantic dust event is associated with both enhanced dust emissions over western North Africa and atmospheric circulation extremes that favor long-range dust transport. An exceptionally strong African easterly jet and associated wave activities export African dust across the Atlantic toward the Caribbean in the middle to lower troposphere, while a westward extension of the North Atlantic subtropical high and a greatly intensified Caribbean low-level jet further transport the descended, shallower dust plume from the Caribbean Basin into the United States. Over western North Africa, increased dust emissions are associated with strongly enhanced surface winds over dust source regions and reduced vegetation coverage in the western Sahel. While there are large uncertainties associated with assessing future trends in African dust emissions, model-projected atmospheric circulation changes in a warmer future generally favor increased long-range transport of African dust to the Caribbean Basin and the United States.
Empirical formulation for multiple groups of primary biological ice nucleating particles from field observations over Amazonia
Authors: Patade Sachin , Phillips Vaughan T. J. , Amato Pierre , Bingemer Heinz G. , Burrows Susannah M. , DeMott Paul J. , Goncalves Fabio L. T. , Knopf Daniel A. , Morris Cindy E. , Alwmark Carl , Artaxo Paulo , Pöhlker Christopher , Schrod Jann , Weber Bettina
Published: April 2021

To resolve the various types of biological ice nuclei (IN) with atmospheric models, an extension of the empirical parameterization (EP) (Phillips et al. 2008; 2013) is proposed to predict the active IN from multiple groups of primary biological aerosol particles (PBAPs). Our approach is to utilize coincident observations of PBAP sizes, concentrations, biological composition, and ice-nucleating ability. The parameterization organizes the PBAPs into five basic groups: fungal spores, bacteria, pollen, viral particles, plant/animal detritus, algae, and their respective fragments. This new biological component of the EP was constructed by fitting predicted concentrations of PBAP IN to those observed at the Amazon Tall Tower Observatory (ATTO) site located in the central Amazon. The fitting parameters for pollen and viral particles, plant/animal detritus, which are much less active as IN than fungal and bacterial groups, are constrained based on their ice nucleation activity from the literature. The parameterization has empirically derived dependencies on the surface area of each group (except algae), and the effects of variability in their mean sizes and number concentrations are represented via their influences on the surface area. The concentration of active algal IN is estimated from literature-based measurements.

Predictions of this new biological component of the EP are consistent with previous laboratory and field observations not used in its construction. The EP scheme was implemented in a 0D parcel model. It confirms that biological IN account for most of the total IN activation at temperatures warmer than −20°C and at colder temperatures dust and soot become increasingly more important to ice nucleation.
Proceedings of the Sleep and Epilepsy Workshop: Section 2 Comorbidities: Sleep Related Comorbidities of Epilepsy
Authors: Pavlova Milena K. , Ng Marcus , Allen Rebecca M. , Boly Melanie , Kothare Sanjeev , Zaveri Hiten , Zee Phyllis C. , Adler Gail , Buchanan Gordon F. , Quigg Mark S. ,   on behalf of the Sleep and Epilepsy Workgroup
Published: April 2021

Epilepsy is a chronic disease with multiple, complex comorbidities. Bidirectional relationships exist among seizures, sleep, circadian rhythms, and diseases within and outside of the central nervous system. Seizures fragment sleep and can contribute to development of sleep disorders, which in turn leads to worse overall health and more seizures. Moreover, treatment options are often limited by interactions with anti-seizure medications. Advances in the fields of epilepsy and in sleep medicine have been made separately, and therefore treating patients with these comorbidities necessitates interdisciplinary approach. The focus of this section of the Sleep and Epilepsy Workgroup was to identify methods of collaboration and outline investigational, educational, and treatment priorities to mutually advance what we consider a combined field.
Visual and Statistical Methods to Calculate Intercoder Reliability for Time-Resolved Observational Research
Authors: Malviya Manoj , Buswell Natascha T. , Berdanier Catherine G. P.
Published: April 2021

While calculating intercoder reliability (ICR) is straightforward for text-based data, such as for interview transcript excerpts, determining ICR for naturalistic observational video data is much more complex. To date, there have been few methods proposed in literature that are robust enough to handle complexities such as the occurrence of simultaneous event complexity and partial agreement by the raters. This is especially important with the emergence of high-resolution video data, which collects nearly continuous or continuous observational data in naturalistic settings. In this paper, we present three approaches to calculating ICR. First, we present the technical approach to clean and compare two coders’ results such that traditional metrics of ICR (e.g., Cohen’s κ, Krippendorff’s α, Scott’s Π) can be calculated, methods previously unarticulated in literature. However, these calculations are intensive, requiring significant data manipulation. As an alternative, this paper also proposes two novel methods to calculate ICR by algorithmically comparing visual representations of each coders’ results. To demonstrate efficacy of the approaches, we employ all three methods on data from two separate ongoing research contexts using observational data. We find that the visual methods perform as well as the traditional measures of ICR and offer significant reduction in the work required to calculate ICR, with an added advantage of allowing the researcher to set thresholds for acceptable agreement in lag time. These methods may transform the consideration of ICR in other studies across disciplines that employ observational data.
Transfer to the clinic: refining forward programming of hPSCs to megakaryocytes for platelet production in bioreactors
Authors: Evans Amanda L. , Dalby Amanda , Foster Holly R. , Howard Daniel , Waller Amie K. , Taimoor Momal , Lawrence Moyra , Mookerjee Souradip , Lehmann Marcus , Burton Annie , Valdez Jorge , Thon Jonathan , Italiano Joseph , Moreau Thomas , Ghevaert Cedric
Published: April 2021

The production of in vitro–derived platelets has great potential for transfusion medicine. Here, we build on our experience in the forward programming (FoP) of human pluripotent stem cells (hPSCs) to megakaryocytes (MKs) and address several aspects of the complex challenges to bring this technology to the bedside. We first identify clinical-grade hPSC lines that generate MKs efficiently. We design a bespoke media to maximize both production and maturity of MKs and improve platelet output. Crucially, we transition the lentiviral-based FoP of hPSCs to a nonviral inducible system. We also show how small molecules promote a definitive hematopoiesis phenotype during the differentiation process, thereby increasing the quality of the final product. Finally, we generate platelets using a bioreactor designed to reproduce the physical cues that promote platelet production in the bone marrow. We show that these platelets are able to contribute to both thrombus formation in vitro and have a hemostatic effect in thrombocytopenic mice in vivo.
scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data
Authors: Ranjan Bobby , Schmidt Florian , Sun Wenjie , Park Jinyu , Honardoost Mohammad Amin , Tan Joanna , Arul Rayan Nirmala , Prabhakar Shyam
Published: April 2021

Background

Clustering is a crucial step in the analysis of single-cell data. Clusters identified in an unsupervised manner are typically annotated to cell types based on differentially expressed genes. In contrast, supervised methods use a reference panel of labelled transcriptomes to guide both clustering and cell type identification. Supervised and unsupervised clustering approaches have their distinct advantages and limitations. Therefore, they can lead to different but often complementary clustering results. Hence, a consensus approach leveraging the merits of both clustering paradigms could result in a more accurate clustering and a more precise cell type annotation.

Results

We presentscConsensus, an$${\mathbf {R}}$$Rframework for generating a consensus clustering by (1) integrating results from both unsupervised and supervised approaches and (2) refining the consensus clusters using differentially expressed genes. The value of our approach is demonstrated on several existing single-cell RNA sequencing datasets, including data from sorted PBMC sub-populations.

Conclusions

scConsensuscombines the merits of unsupervised and supervised approaches to partition cells with better cluster separation and homogeneity, thereby increasing our confidence in detecting distinct cell types.scConsensusis implemented in$${\mathbf {R}}$$Rand is freely available on GitHub athttps://github.com/prabhakarlab/scConsensus.
Performance improvement for a 2D convolutional neural network by using SSC encoding on protein–protein interaction tasks
Authors: Wang Yang , Li Zhanchao , Zhang Yanfei , Ma Yingjun , Huang Qixing , Chen Xingyu , Dai Zong , Zou Xiaoyong
Published: April 2021

Background

The interactions of proteins are determined by their sequences and affect the regulation of the cell cycle, signal transduction and metabolism, which is of extraordinary significance to modern proteomics research. Despite advances in experimental technology, it is still expensive, laborious, and time-consuming to determine protein–protein interactions (PPIs), and there is a strong demand for effective bioinformatics approaches to identify potential PPIs. Considering the large amount of PPI data, a high-performance processor can be utilized to enhance the capability of the deep learning method and directly predict protein sequences.

Results

We propose the Sequence-Statistics-Content protein sequence encoding format (SSC) based on information extraction from the original sequence for further performance improvement of the convolutional neural network. The original protein sequences are encoded in the three-channel format by introducing statistical information (the second channel) and bigram encoding information (the third channel), which can increase the unique sequence features to enhance the performance of the deep learning model. On predicting protein–protein interaction tasks, the results using the 2D convolutional neural network (2D CNN) with the SSC encoding method are better than those of the 1D CNN with one hot encoding. The independent validation of new interactions from the HIPPIE database (version 2.1 published on July 18, 2017) and the validation of directly predicted results by applying a molecular docking tool indicate the effectiveness of the proposed protein encoding improvement in the CNN model.

Conclusion

The proposed protein sequence encoding method is efficient at improving the capability of the CNN model on protein sequence-related tasks and may also be effective at enhancing the capability of other machine learning or deep learning methods. Prediction accuracy and molecular docking validation showed considerable improvement compared to the existing hot encoding method, indicating that the SSC encoding method may be useful for analyzing protein sequence-related tasks. The source code of the proposed methods is freely available for academic research athttps://github.com/wangy496/SSC-format/.
Long-term TE persistence even without beneficial insertion
Authors: Kremer Stefan C. , Linquist Stefan , Saylor Brent , Elliott Tyler A. , Gregory T. Ryan , Cottenie Karl
Published: April 2021

This correspondence responds to the critique by Butler et al. (BMC Genomics 22:241, 2021) of our recent paper on transposable element (TE) persistence. We address the three main objections raised by Butler et al. After running a series of additional simulations that were inspired by the authors’ criticisms, we are able to present a more nuanced understanding of the conditions that generate long-term persistence.
Characterization and transcriptomic analysis of a novel yellow-green leaf wucai (Brassica campestris L.) germplasm
Authors: Nie Libing , Zheng Yushan , Zhang Liting , Wu Ying , Zhu Shidong , Hou Jinfeng , Chen Guohu , Tang Xiaoyan , Wang Chenggang , Yuan Lingyun
Published: April 2021

Background

Leaf color mutants are the ideal materials to explore the pathways of chlorophyll (Chl) metabolism, chloroplast development, and photosynthesis system. In this study, a spontaneous yellow-green leaf wucai (Brassica campestris L.) mutant “WY16–13” was identified, which exhibited yellow-green leaf color during its entire growth period. However, current understanding of the molecular mechanism underlying Chl metabolism and chloroplast development of “WY16–13” is limited.

Results

Total Chl and carotenoid content in WY16–13 was reduced by 60.92 and 58.82%, respectively, as compared with its wild type parental line W16–13. Electron microscopic investigation revealed fewer chloroplasts per cell and looser stroma lamellae in WY16–13 than in W16–13. A comparative transcriptome profiling was performed using leaves from the yellow-green leaf type (WY16–13) and normal green-leaf type (W16–13). A total of 54.12 million (M) (WY16–13) and 56.17 M (W16–13) reads were generated. A total of 40,578 genes were identified from the mapped libraries. We identified 3882 differentially expressed genes (DEGs) in WY16–13 compared with W16–13 (i.e., 1603 upregulated genes and 2279 downregulated genes). According to the Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, these DEGs are involved in porphyrin and Chl metabolism [i.e., chlorophyllase (CLH), heme oxygenase (HO), chlorophyll (ide) b reductase (NYC), and protochlorophyllide oxidoreductase (POR) genes], carbohydrate metabolism, photosynthesis, and carbon fixation in photosynthetic organisms. Moreover, deficiency in Chl biosynthetic intermediates in WY16–13 revealed that the formation of the yellow-green phenotype was related to the disorder of heme metabolism.

Conclusions

Our results provide valuable insights into Chl deficiency in the yellow-green leaf mutant and a bioinformatics resource for further functional identification of key allelic genes responsible for differences in Chl content.
Proteomic response of Escherichia coli to a membrane lytic and iron chelating truncated Amaranthus tricolor defensin
Authors: Moyer Tessa B. , Purvis Ashleigh L. , Wommack Andrew J. , Hicks Leslie M.
Published: April 2021

Background

Plant defensins are a broadly distributed family of antimicrobial peptides which have been primarily studied for agriculturally relevant antifungal activity. Recent studies have probed defensins against Gram-negative bacteria revealing evidence for multiple mechanisms of action including membrane lysis and ribosomal inhibition. Herein, a truncated synthetic analog containing the γ-core motif ofAmaranthus tricolorDEF2 (Atr-DEF2) reveals Gram-negative antibacterial activity and its mechanism of action is probed via proteomics, outer membrane permeability studies, and iron reduction/chelation assays.

Results

Atr-DEF2(G39-C54) demonstrated activity against two Gram-negative human bacterial pathogens,Escherichia coliandKlebsiella pneumoniae. Quantitative proteomics revealed changes in theE. coliproteome in response to treatment of sub-lethal concentrations of the truncated defensin, including bacterial outer membrane (OM) and iron acquisition/processing related proteins. Modification of OM charge is a common response of Gram-negative bacteria to membrane lytic antimicrobial peptides (AMPs) to reduce electrostatic interactions, and this mechanism of action was confirmed for Atr-DEF2(G39-C54) via an N-phenylnaphthalen-1-amine uptake assay. Additionally, in vitro assays confirmed the capacity of Atr-DEF2(G39-C54) to reduce Fe3+and chelate Fe2+at cell culture relevant concentrations, thus limiting the availability of essential enzymatic cofactors.

Conclusions

This study highlights the utility of plant defensin γ-core motif synthetic analogs for characterization of novel defensin activity. Proteomic changes inE. coliafter treatment with Atr-DEF2(G39-C54) supported the hypothesis that membrane lysis is an important component of γ-core motif mediated antibacterial activity but also emphasized that other properties, such as metal sequestration, may contribute to a multifaceted mechanism of action.
Preoperative X-ray C2C6AR is applicable for prediction of difficult laryngoscopy in patients with cervical spondylosis
Authors: Zhou Yang , Han Yongzheng , Li Zhengqian , Zhao Yuqing , Yang Ning , Liu Taotao , Li Min , Wang Jun , Guo Xiangyang , Xu Mao
Published: April 2021

Background

Airway management is one of the most important techniques in anesthesia practice and inappropriate airway management is related with airway injury, brain hypoxia, and even death. The patients with cervical spondylosis are often confronted with difficult laryngoscopy who are more prone to appear difficult airway, so it is important to figure out valuable predictors of difficult laryngoscopy in these patients.

Methods

We randomly enrolled 270 patients undergoing elective cervical spine surgery and analyzed the cervical mobility data in predicting difficult laryngoscopy. The preoperative X-ray radiological indicators were measured by an attending radiologist. Cormack-Lehane scales were assessed during intubation, and patients with a class III or IV view were assigned to the difficult laryngoscopy group.

Results

Univariate analysis showed that the hyomental distance (HMD, the distance between the hyoid bone and the tip of the chin) and the hyomental distance ratio (HMDR, the ratio between HMD in the extension position and the one in the neutral position) might not be suitable indicators in patients with cervical spondylosis. Binary multivariate logistic regression (backward-Wald) analyses identified two independent correlative factors from the cervical mobility indicators that correlated best as a predictor of difficult laryngoscopy: modified Mallampati test (MMT) and C2C6AR (the ratio of the angle between a line passing through the bottom of the second cervical vertebra and a line passing through the bottom of the sixth cervical vertebra in the extension position and the one in the neutral position). The odds ratio (OR) and 95 % CI were 2.292(1.093–4.803) and 0.493 (0.306–0.793), respectively. C2C6AR exhibited the largest area under the curve (0.714; 95 % CI 0.633–0.794).

Conclusions

C2C6AR based on preoperative X-ray images may be the most accurate predictor of cervical mobility indicators for difficult laryngoscopy in patients with cervical spondylosis.

Trial registration

The study was registered at the Chinese Clinical Trial Registry (http://www.chictr.org.cn; identifier: ChiCTR-ROC-16,008,598) on June 6, 2016.
Golimumab improves work productivity in patients suffering from moderate to severe ulcerative colitis: results of a prospective study over 24 months
Authors: Teich Niels , Grümmer Harald , Jörgensen Eric , Liceni Thomas , Holtkamp-Endemann Frank , Fischer Tim , Hohenberger Susanne
Published: April 2021

Background

Ulcerative colitis (UC) is a chronic inflammatory bowel disease with recurrent episodes of debilitating symptoms negatively affecting work productivity and health-related quality of life (HRQoL). The use of biologics in UC treatment improves work and HRQoL but prospective long-term data concerning the treatment with TNFα inhibitor golimumab in UC patients are still rare. Therefore, our study aimed to evaluate the change in work productivity, capacity for daily activities and HRQoL in UC patients treated with golimumab in Germany.

Methods

Using the Work Productivity and Activity Impairment questionnaire, the change in work productivity and in capacity for daily activities after 3 months and over the whole observational period of 24 months were assessed (both primary endpoints). Disease-specific and health-related quality of life (QoL) were analyzed with the Inflammatory Bowel Disease Questionnaire (IBDQ), the Short-Form 12 Health Survey Questionnaire (SF-12), and the Partial Mayo Score (secondary endpoints). Further, disease-related hospitalization rates were assessed.

Results

This prospective non-interventional study included 286 patients. Thereof, 212 patients were employed at baseline (modified intention to treat analysis set employed at baseline, mITTe). 61.3% of the mITTe patients had moderate and 17.0% had severe UC. Three months after initiation of golimumab therapy, total work productivity impairment (TWPI) score and activity impairment score improved significantly from baseline with a mean change of − 17.3% (p < 0.0001) and − 14.4% (p < 0.0001), respectively. Results persisted over 24 months (mean change TWPI score: − 24.5%, mean change activity impairment score: − 30.0%). Disease- and health-related QoL also improved significantly under golimumab treatment as indicated by increased IBDQ [mean change: 28.0 (SD: ± 36.1, month 3), 42.1 (SD: ± 39.5, month 24)] and SF-12 scores [PCS-12: 45.9 (SD: ± 8.5), MCS-12: 4.9 (SD: ± 10.6, month 3), PCS-12: 5.9 (SD: ± 9.0), MCS-12: 6.4 (SD: ± 11.1, month 24)]. Disease-related hospitalization rate decreased from 16.0% (BL) to 4.3% at month 24 and the mean number of missed working days due to UC decreased from 8.2 (SD: 17.6, BL) to 0.7 (SD: 2.1) after golimumab induction.

Conclusions

Golimumab leads to notable long-term improvements in work productivity, daily activity, HRQoL, and disease-related hospitalization rates in patients with moderate to severe UC.

Trial registration: PEI (Paul-Ehrlich-Institute, Langen, Germany) Registration Nr: NIS#255 (https://www.pei.de/SharedDocs/awb/nis-0201-0300/0255.html)