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Copyright of Przegląd Elektrotechniczny is the property of Przeglad Elektrotechniczny and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

An analysis is performed to examine trends in temperature, relative humidity, and wind-speed over the Indian landmass and in the isles of Lakshadweep (Arabian Sea side) and Andaman and Nicobar (Bay of Bengal side) over the last four decades (from 1981 to 2021). MERRA data deployed for revealing the large-scale fluctuations and linear trends in these parameters covering 36 locations. Surface temperature (2 m above ground) data showed a linear rise, which is more prominent after 2000, both in the Arabian side and the Bay of Bengal. Over this period, temperature increased ~ 0.7–0.8 °C on both sides of Indian landmass. About two third locations (24 locations) in the study showed increase in temperature. However, relative humidity data on all island locations exhibited a decrease (prominent during 2000–2021). Quasi-periodic fluctuations in temperature (which is linearly rising) closely relates with the ENSO parameter (correlation coefficient 'r' in Arabian Sea and Andaman and Nicobar ranged from ~ 0.20 to 0.34; which is statistically significant and relatively larger towards Andaman Islands). 'r' increased considerably (> 0.5) during 2000–2021. Wind-speed, in general, showed larger magnitude over Andaman and Nicobar Islands (~ 5.0 m/s yearly averaged) in comparison to Arabian Sea (~ 4.0 m/s) and landmass (~ 2.2 m/s). On the other hand, solar cycle (sun spot numbers) and wind-speed reflects a weak positive correlation coefficient (< ~ 0.40) but statistically significant while no consequential correlation found between solar cycle and relative humidity. Detailed analysis suggests that relative humidity decreased both over landmass and islands during 2000–2021. Interestingly, surface temperature increased more rapidly between latitudes 7.03°N and 12.91°N after 2000. Rise in temperature and long period fluctuations (> 2–3 years) in the lower latitudes (< 15°N) showed a strong association with ENSO signal suggesting invigorated atmosphere ocean interaction. [ABSTRACT FROM AUTHOR]

Copyright of Przegląd Elektrotechniczny is the property of Przeglad Elektrotechniczny and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

• Proposed-1: Forecast of Solar Cycle 25 using Hybrid CNN-Bidirectional-GRU(CNN-BiGRU). • Proposed-2: Novel Gradient Residual Correction (GRC) model to enhance the proposed-1. • Models are compared with deep-learning traditional models over 4-types of SSN data. • Models' performances are validated based on Friedman ranking for measures. In this study, a hybrid deep-learning(DL) model is proposed, which consists of a Convolution-Neural-Network (CNN) and Bidirectional-Gated-Recurrent-Unit (Bi-GRU) for the prediction of sunspot numbers(SSN) of different frequencies along with novel post-processing techniques of Gradient-Residual-Correction (GRC) to enhance the accuracy of the predictions further. GRC is utilized to reduce the residual present in the forecasted values. The AdaBoost regression model is implemented over the residual obtained from the prediction of training data using a hybrid CNN-BiGRU model with respect to the gradient of the training data points to predict the residual for the test data points. Ultimately, the predicted residual for test data points is summed up with the predicted test data points to achieve the final predictions. The results obtained from the proposed methods are compared with the results obtained from traditional DL models. The validation of the proposed method is carried out based on four performance metrics, namely Root Mean Squared Error(RMSE), Mean Absolute Scaled Error(MASE), Mean Absolute Error(MAE), and Mean Absolute Percentage Error(MAPE). A significant percentage of improvement is observed while using the GRC technique in comparison to all other experimented models for all four variants of SSN data. A maximum improvement of 85.71% has been achieved in comparison to the BiLSTM model over the 13-month smoothed SSN dataset on the basis of MAPE. Friedman Ranking is also performed as a non-parametric statistical test over the results of the performance measures. This model has been utilized for the forecast of solar cycle 25(SC25) over the annual mean of total SSN. It has been observed that the SC25 is expected to reach its peak in the year 2024 with an annual average peak value of 143.641. Comparative analysis of SC25 and the peak of SSN in the ongoing cycle with the previous works are also carried out. [ABSTRACT FROM AUTHOR]

Electronic circuits must address electromagnetic interference due to high-speed transmissions and simultaneous switching actions. This paper proposes a design of novel planar EBG structure L Bridge with embedded slit type with 3 × 3 array fashion, which can be used in a plane layer of a printed circuit board to reduce simultaneous switching noise (SSN). Two sets of pattern such as alternate structure and entire embedded pattern are considered and measured the cut-off frequencies. The performance of the structure is simulated, experimentally verified using R&S®ZVH Vector Network Analyser for the frequency range 0.1 to 10 GHz and compared the outcomes. It is observed that for the −50 dB of noise depth, proposed structure is achieved 1.6 GHz to 10 GHz as lower and upper cut-off frequency. In addition, this concluded the noise suppression using equivalent circuit model and parallel plate wave guide theory. Signal integrity on this structure is also analysed with single-ended and differential mode signal transition. Eye pattern is generated and compared for measuring and validating the signal quality while using this EBG structure. [ABSTRACT FROM AUTHOR]

In this paper, an optimized long short-term memory (LSTM) model is proposed to deal with the smoothed monthly F 10.7 data, aiming to predict the peak amplitude of F 10.7 and the occurring time for Solar Cycle 25 (SC-25) to obtain the maximum amplitude of sunspot number (SSN) and the reaching time. The "re-prediction" process in the model uses the latest prediction results obtained from the previous prediction as the input for the next prediction calculation. The prediction errors between the predicted and observed peak amplitude of F 10.7 for SC-23 and SC-24 are 2.87% and 1.09%, respectively. The predicted peak amplitude of F 10.7 for SC-25 is 156.3, and the maximum value of SSN is calculated as 147.9, which implies that SC-25 will be stronger than SC-24. SC-25 will reach its peak in July 2025. [ABSTRACT FROM AUTHOR]

Copyright of Listy Cukrovarnicke a Reparske is the property of VUC Praha a.s. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In this research, the plasma parameters of the ionospheric F-layer have been calculated during daytime at 12 PM condition for four different months (January, April, July and October) over Iraqi capital “ Baghdad” (44.3° E, 33.3° N) during the year 2019 that represents the beginning of the solar cycle 25. Depending on the impact of the solar activity that was represented by the number of sunspot (SSN) and solar flux (F10.7 cm) on the variation and behavior of the electron density (ne) and the electron temperature (Te) which have been conducted using the international reference ionosphere (IRI 2016) model which was considered as one of the recommended international models for different heights (150 500) km with 50 km increment. It has been noticed that the seasonal variations of electron density (ne) and frequency (fpe) around the equinoxes are higher than those in summer and winter for solar minimum (2019).While λDe around the equinoxes (April and October) is lower than that of summer and winter for solar minimum (2019). It has been explained as a positive correlation between the thermal velocity of electron (υte) and (Te) in all seasonal variation of ionosphere for the selected year. In this paper, the weakness of the electron coupling parameter in the ionosphere was proved in all seasons of the year 2019. [ABSTRACT FROM AUTHOR]

El valor b de la distribución Gutenberg-Richter es una de las herramientas más importantes para estudios de peligro sísmico; dicho valor es de gran utilidad para estimar razones de ocurrencia de sismos, y está relacionado también con niveles de esfuerzo del medio y presenta cambios precursores a la ocurrencia de grandes sismos. Sin embargo, determinaciones correctas y confiables del valor b dependen críticamente de contar con muestras suficientes. Llevamos a cabo estudios orientados a corroborar si efectivamente ocurren cambios precursores del valor b antes de sismos grandes (M ≥ 7.0) a lo largo de la zona de subducción de México; estos estudios fueron basados en datos del catálogo del Servicio Sismológico Nacional (SSN) de 1988 a 2018. Lo resultados para cinco grandes sismos sugieren que los cambios precursores efectivamente existen, pero las diferencias entre los valores obtenidos no son estadísticamente significativas debido a las incertidumbres causadas porque el SSN usa diferentes escalas de magnitud para sismos pequeños (bajo M ~4.5) y para medianos a grandes (arriba de M ~4.5). Discutimos algunas limitaciones sobre la aplicabilidad de los datos del SSN. doi: https://doi.org/10.22201/igeof.00167169p.2020.59.4.2019

Currently, a social security number (SSN) is held by almost every legal resident of the United States and works as an important numbering system. However, this was not the case in the early years of the Social Security program and historical changes in SSN holder rates had not been examined sufficiently. It is important to understand the changes in health policies and situations. Thus, the present article examined historical changes in the rates of SSN holders in the United States between 1909 and 2019. Analyses demonstrated that the rates clearly increased. Specifically, in Phase 1 (1909-1919), the rates were low in the early period, but they increased markedly. In Phase 2 (1919-1952), the rates continued to increase gradually. In Phase 3 (1952-2019), the rates were almost 100% and reached saturation. This basic information leads to a better understanding of the health policies and situations, contributing to medical and social science research.

Purpose: The objective of this analysis was to compare the cost per responder between risankizumab and secukinumab among patients with moderate-to-severe plaque psoriasis in Italy. Methods: The clinical efficacy was assessed based on IMMerge study of published efficacy data as measured by Psoriasis Area and Severity Index response (PASI 90 and PASI 100) for risankizumab and secukinumab. The treatment cost was based on the number of administrations dispensed in the first (induction plus maintenance period) and the second (maintenance period only) year of treatment and the ex-factory price of each treatment. The cost per responder was adopted as a cost-effectiveness indicator. Results: Independently of the PASI response (PASI 90 and PASI 100) used and the year of treatment considered, the cost per responder was consistently lower for risankizumab compared to secukinumab in all clinical measures. For example, considering the first-year costs and PASI 100, the cost per responder for risankizumab was € 24,506.83 compared to € 38,000.00 for secukinumab. The differences in the cost per responder between risankizumab and secukinumab increased when higher PASI response levels were considered. Conclusion: This economic evaluation suggested that the cost per responder is consistently lower for risankizumab compared to secukinumab from the perspective of the Italian National Health Service in the treatment of moderate-to-severe plaque psoriasis.

Background: Arthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have evolved. The Toll pathway, involved in the innate immune system, was first described as part of the developmental pathway for dorsal-ventral differentiation in Drosophila. Its later discovery in vertebrates suggested that this system was extremely conserved. However, there is variation in presence/absence, copy number and sequence divergence in various genes along the pathway. As most studies have only focused on Diptera, for a comprehensive and accurate homology-based approach it is important to understand gene function in a number of different species and, in a group as diverse as insects, the use of species belonging to different taxonomic groups is essential. Results: We evaluated the diversity of Toll pathway gene families in 39 Arthropod genomes, encompassing 13 different Insect Orders. Through computational methods, we shed some light into the evolution and functional annotation of protein families involved in the Toll pathway innate immune response. Our data indicates that: 1) intracellular proteins of the Toll pathway show mostly species-specific expansions; 2) the different Toll subfamilies seem to have distinct evolutionary backgrounds; 3) patterns of gene expansion observed in the Toll phylogenetic tree indicate that homology based methods of functional inference might not be accurate for some subfamilies; 4) Spatzle subfamilies are highly divergent and also pose a problem for homology based inference; 5) Spatzle subfamilies should not be analyzed together in the same phylogenetic framework; 6) network analyses seem to be a good first step in inferring functional groups in these cases. We specifically show that understanding Drosophila's Toll functions might not indicate the same function in other species. Conclusions: Our results show the importance of using species representing the different orders to better understand insect gene content, origin and evolution. More specifically, in intracellular Toll pathway gene families the presence of orthologues has important implications for homology based functional inference. Also, the different evolutionary backgrounds of Toll gene subfamilies should be taken into consideration when functional studies are performed, especially for TOLL9, TOLL, TOLL2_7, and the new TOLL10 clade. The presence of Diptera specific clades or the ones lacking Diptera species show the importance of overcoming the Diptera bias when performing functional characterization of Toll pathways. [ABSTRACT FROM AUTHOR]

In this study the statistics of ionospheric total electron content (TEC), derived from a GSV4004B dual-frequency Global Positioning System (GPS) receiver at Agartala station (23.450°N, 91.150°E) located in northern equatorial ionization anomaly (EIA) crest region of the Indian subcontinent, is reported with a performance analysis of IRI-2016 and IRI-2012 models during the ascending, maxima, declining and minima phases (2013-2018) of the solar cycle 24. Variations of model total electron content, as obtained from the IRI-2016 and IRI-2012 for the three options of topside electron density namely NeQuick, IRI 2001 and IRI 01-corr, are compared with the observed total electron content during different periods of interest viz. monthly, seasonal, annual and the correlations with solar activity parameters viz. sunspot number (SSN), 10.7 cm solar radio flux (F10.7), solar EUV flux, are also investigated. All the three options of IRI-2016 and IRI-2012 models show an earlier occurrence of diurnal maximum total electron content, as compared to the observed diurnal maximum GPS total electron content, throughout all the months during the complete period of observation. As the solar activity decreases (from 2015 to 2018), the model starts underestimating GPS total electron content, which becomes significantly high during the very low solar activity period of 2017-18 for all the months. IRI-2016 model underestimates the GPS total electron content before the hours of diurnal maximum and overestimates after the hours of diurnal maximum in the years from 2013-2018. IRI-2012 model underestimates the GPS total electron content before the hours of diurnal maximum and overestimates after the hours of diurnal maximum in the years from 2013-17 but overestimate during the whole day in the year of 2018. Overestimation by IRI-2012 is much more than that by IRI-2016 in the year of 2018. Predictions given by IRI-2016 are better than that given by IRI-2012 for our region. The seasonal mean maximum total electron content values are highest during the spring equinox months and lowest during the winter months except the year of 2014 and 2013. The correlation analysis, between the GPS total electron content and solar indices, show that the correlation coefficient is higher for the solar EUV flux, as compared to the sunspot number (SSN) and 10.7 cm solar radio flux (F10.7). [ABSTRACT FROM AUTHOR]

Space debris monitoring is nowadays a priority for worldwide space agencies, due to the serious threat that these objects present. More and more efforts have been made to extend the network of available radar systems devoted to the control of space. A meticulous review has been done in this paper, in order to find and classify the considerable amounts of data provided by the scientific community that deal with RADAR measurement for the debris monitoring and tracking. The information gathered is organized based on the volume of found data and classified taking into account the geographical location of the facilities. [ABSTRACT FROM AUTHOR]

Purpose: The objective of this analysis was to compare the cost per responder between risankizumab and secukinumab among patients with moderate-to-severe plaque psoriasis in Italy. Methods: The clinical efficacy was assessed based on IMMerge study of published efficacy data as measured by Psoriasis Area and Severity Index response (PASI 90 and PASI 100) for risankizumab and secukinumab. The treatment cost was based on the number of administrations dispensed in the first (induction plus maintenance period) and the second (maintenance period only) year of treatment and the ex-factory price of each treatment. The cost per responder was adopted as a cost-effectiveness indicator. Results: Independently of the PASI response (PASI 90 and PASI 100) used and the year of treatment considered, the cost per responder was consistently lower for risankizumab compared to secukinumab in all clinical measures. For example, considering the first-year costs and PASI 100, the cost per responder for risankizumab was € 24,506.83 compared to € 38,000.00 for secukinumab. The differences in the cost per responder between risankizumab and secukinumab increased when higher PASI response levels were considered. Conclusion: This economic evaluation suggested that the cost per responder is consistently lower for risankizumab compared to secukinumab from the perspective of the Italian National Health Service in the treatment of moderate-to-severe plaque psoriasis. [ABSTRACT FROM AUTHOR]

Copyright of Technical Transactions / Czasopismo Techniczne is the property of Sciendo and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The paper presents an approach which combines the concept of macro-level BIM-based cost analyzes and application of artificial intelligence tools – namely artificial neural networks. Discussion and foundations of the proposed approach are introduced in the paper to clarify the problem’s core. An exemplary case study reports the results of initial studies on the application of neural networks for the purposes of BIM-based cost analysis of a buildings’ floor structural frame. The results obtained justify the proposal of application of neural networks as a supportive mathematical tool in the problem presented in the paper.

Abstract Background Large enzyme families may contain functionally diverse members that give rise to clusters in a sequence similarity network (SSN). In prokaryotes, the genome neighborhood of a gene-product is indicative of its function and thus, a genome neighborhood network (GNN) deduced for an SSN provides strong clues to the specific function of enzymes constituting the different clusters. The Enzyme Function Initiative ( http://enzymefunction.org/ ) offers services that compute SSNs and GNNs. Results We have implemented AGeNNT that utilizes these services, albeit with datasets purged with respect to unspecific protein functions and overrepresented species. AGeNNT generates refined GNNs (rGNNs) that consist of cluster-nodes representing the sequences under study and Pfam-nodes representing enzyme functions encoded in the respective neighborhoods. For cluster-nodes, AGeNNT summarizes the phylogenetic relationships of the contributing species and a statistic indicates how unique nodes and GNs are within this rGNN. Pfam-nodes are annotated with additional features like GO terms describing protein function. For edges, the coverage is given, which is the relative number of neighborhoods containing the considered enzyme function (Pfam-node). AGeNNT is available at https://github.com/kandlinf/agennt . Conclusions An rGNN is easier to interpret than a conventional GNN, which commonly contains proteins without enzymatic function and overly specific neighborhoods due to phylogenetic bias. The implemented filter routines and the statistic allow the user to identify those neighborhoods that are most indicative of a specific metabolic capacity. Thus, AGeNNT facilitates to distinguish and annotate functionally different members of enzyme families.

Abstract This study aimed at identifying in: (1) planning the classroom management for the SSN classes and (2) managing the classroom, in the teaching and learning process of science in SSN schools.This is a evaluatif study which focuses on the classroom management of science learning in SSN junior high schools. The subjects of the research are SSN Junior High Schools of Pati Regency which focuses on the classroom management of science learning. There are six SSN schools, namely SMP N 2 Pati, SMP N 4 Pati, SMP N 1 Wedarijaksa, SMP N 1 Trangkil, SMP N 1 Tlogowungu, and SMP N 1 Gabus. The data were gained through observation, interview, questionnaire, and document study.The result shows that : the classroom management planning in SSN Junior High Schools in the science learning at Pati Regency are categorizes good: the science teacher SSN Junior High School the use of ICT in science learning was not taken into account, teaching materials (handouts, worksheets, modules and ICT-based teaching material) were not developed yet, the assessment planning did not complete. Process in the science learning at SNN junior High School are as categirizes good. Keywords: Classroom Management, SSN, Science Learning. Abstrak Penelitian ini bertujuan untuk: (1) mengidentifikasi perencanaan pengelolaan kelas di SMP SSN dalam pembelajaran sains; (2) mengidentifikasi proses pengelolaan kelas di SMP SSN dalam pembelajaran sains. Penelitian ini merupakan penelitian evaluatif, yang memfokuskan pada kualitas pengelolaan kelas pembelajaran sains pada SMP SSN. Subjek penelitian ini SMP SSN Kabupaten Pati yang difokuskan pada perencanaan dan pelaksanaan pengelolaan kelas pembelajaran sains.Data penelitian diperoleh melalui: observasi, wawancara, angket, dan dokumentasi. Data yang diperoleh bersifat subjektif, berupa hasil observasi, wawancara, dan angket.Hasil penelitian menunjukkan: perencanaan pengelolaan kelas di SMP SSN dalam pembelajaran sains berkategori baik. Guru sains di SMP Kategori SSN belum sepenuhnya mempertimbangkan penerapan TIK dalam pembelajaran IPA,belum mengembangkan bahan ajar sendiri dalam berbagai bentuk, baik handout, LKS, modul dan bahan ajar yang lain, serta belum merencanakan penilaian dengan lengkap, baru menuliskan teknik penilaian belum menyertakan instrumen penilaian dan rubrik penilaian.Pelaksanaan pengelolaan kelas di SMP SSN dalam pembelajaran sains berkategori baik. Guru sains di SMP Kategori SSN belum sepenuhnya menerapkan pembelajaran berbasis CTL, serta pembelajaran sains yang dilakukan belum sepenuhnya memanfaatkan media ICT.Guru sains di SMP Kategori SSN belum sepenuhnya menerapkan pembelajaran berbasis CTL, serta pembelajaran sains yang dilakukan belum sepenuhnya memanfaatkan media ICT. Kata Kunci: Pengelolaan Kelas, SSN, Pembelajaran Sains.

Space debris monitoring is nowadays a priority for worldwide space agencies, due to the serious threat that these objects present. More and more efforts have been made to extend the network of available radar systems devoted to the control of space. A meticulous review has been done in this paper, in order to find and classify the considerable amounts of data provided by the scientific community that deal with RADAR measurement for the debris monitoring and tracking. The information gathered is organized based on the volume of found data and classified taking into account the geographical location of the facilities.

The ionosphere provides a channel that is able to propagate electromagnetic waves for long-haul communications, allowing Non-Line-Of-Sight (NLOS) radio communications in the high-frequency band (HF). Nonetheless, its performance as a communications channel mainly depends on solar activity, as Earth’s diurnal and seasonal cycles modify the ionospheric ionization by the sun and consequently the channel performance. La Salle and the Observatori de l’Ebre have conducted oblique soundings of a 12,760 km ionospheric channel from Livingston Island (South Shetland Archipelago—Antarctica −62.7∘S, 299.6∘E) to Cambrils (Spain −41.0∘N, 1.0∘E) to evaluate this evidence and analyze the characteristics of this particular channel. The final goal of the project is to establish a stable communications link to be used as a backup for low throughput data transmission from the various geomagnetic and meteorological sensors located in the Spanish Antarctic Station. The aim of this paper is to confirm the relationship between the channel availability of narrowband and wideband communications and the resulting channel parameters with the solar and ionospheric activity for four consecutive sounding campaigns.

Concurrency control (CC) algorithms must trade off strictness for performance. In particular, serializable CC schemes generally pay higher cost to prevent anomalies, both in runtime overhead such as the maintenance of lock tables and in efforts wasted by aborting transactions. We propose the serial safety net (SSN), a serializability-enforcing certifier which can be applied on top of various CC schemes that offer higher performance but admit anomalies, such as snapshot isolation and read committed. The underlying CC mechanism retains control of scheduling and transactional accesses, while SSN tracks the resulting dependencies. At commit time, SSN performs a validation test by examining only direct dependencies of the committing transaction to determine whether it can commit safely or must abort to avoid a potential dependency cycle. SSN performs robustly for a variety of workloads. It maintains the characteristics of the underlying CC without biasing toward a certain type of transactions, though the underlying CC scheme might. Besides traditional OLTP workloads, SSN also efficiently handles heterogeneous workloads which include a significant portion of long, read-mostly transactions. SSN can avoid tracking the vast majority of reads (thus reducing the overhead of serializability certification) and still produce serializable executions with little overhead. The dependency tracking and validation tests can be done efficiently, fully parallel and latch-free, for multi-version systems on modern hardware with substantial core count and large main memory. We demonstrate the efficiency, accuracy and robustness of SSN using extensive simulations and an implementation that overlays snapshot isolation in ERMIA, a memory-optimized OLTP engine that supports multiple CC schemes. Evaluation results confirm that SSN is a promising approach to serializability with robust performance and low overhead for various workloads. [ABSTRACT FROM AUTHOR]

Background: Large enzyme families may contain functionally diverse members that give rise to clusters in a sequence similarity network (SSN). In prokaryotes, the genome neighborhood of a gene-product is indicative of its function and thus, a genome neighborhood network (GNN) deduced for an SSN provides strong clues to the specific function of enzymes constituting the different clusters. The Enzyme Function Initiative (http://enzymefunction.org/) offers services that compute SSNs and GNNs. Results: We have implemented AGeNNT that utilizes these services, albeit with datasets purged with respect to unspecific protein functions and overrepresented species. AGeNNT generates refined GNNs (rGNNs) that consist of cluster-nodes representing the sequences under study and Pfam-nodes representing enzyme functions encoded in the respective neighborhoods. For cluster-nodes, AGeNNT summarizes the phylogenetic relationships of the contributing species and a statistic indicates how unique nodes and GNs are within this rGNN. Pfam-nodes are annotated with additional features like GO terms describing protein function. For edges, the coverage is given, which is the relative number of neighborhoods containing the considered enzyme function (Pfam-node). AGeNNT is available at https://github.com/kandlinf/agennt. Conclusions: An rGNN is easier to interpret than a conventional GNN, which commonly contains proteins without enzymatic function and overly specific neighborhoods due to phylogenetic bias. The implemented filter routines and the statistic allow the user to identify those neighborhoods that are most indicative of a specific metabolic capacity. Thus, AGeNNT facilitates to distinguish and annotate functionally different members of enzyme families. [ABSTRACT FROM AUTHOR]

One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced. [ABSTRACT FROM AUTHOR]

Key message: A method based on DNA single-strand conformation polymorphism is demonstrated for effective genotyping of CRISPR/Cas9-induced mutants in rice. Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) has been widely adopted for genome editing in many organisms. A large proportion of mutations generated by CRISPR/Cas9 are very small insertions and deletions (indels), presumably because Cas9 generates blunt-ended double-strand breaks which are subsequently repaired without extensive end-processing. CRISPR/Cas9 is highly effective for targeted mutagenesis in the important crop, rice. For example, homozygous mutant seedlings are commonly recovered from CRISPR/Cas9-treated calli. However, many current mutation detection methods are not very suitable for screening homozygous mutants that typically carry small indels. In this study, we tested a mutation detection method based on single-strand conformational polymorphism (SSCP). We found it can effectively detect small indels in pilot experiments. By applying the SSCP method for CRISRP-Cas9-mediated targeted mutagenesis in rice, we successfully identified multiple mutants of OsROC5 and OsDEP1. In conclusion, the SSCP analysis will be a useful genotyping method for rapid identification of CRISPR/Cas9-induced mutants, including the most desirable homozygous mutants. The method also has high potential for similar applications in other plant species. [ABSTRACT FROM AUTHOR]