bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectral Efficient Blind Channel Estimation Technique for MIMO-OFDM Communications
Authors: Bhandari Renuka , Jadhav Sangeeta
Published: March 2020

With emerge of increasing research in the domain of future wireless communications, massive MIMO (multiple inputs multiple outputs) attracted most of researchers interests. Massive MIMO is high-speed wireless communication standards. A channel estimation technology plays the essential role in the MIMO systems. Efficient channel estimation leads to spectral efficient wireless communications. The critics of Inter-Symbol Interference (ISI) are the challenging tasks while designing the channel estimation methods. To mitigate the challenges of ISI, we proposed the novel blind channel estimation method which based on Independent component analysis (ICA) in this paper. Proposed channel estimation it works for both blind interference cancellation and ISI cancellation. The proposed Hybrid ICA (HICA) method depends on pulse shape filtering and ambiguity removal to improve the spectral efficiency and reliability for MIMO communications. The Kurtosis operation is used to measure the complex data at first to estimate the common signals. Then we exploited the advantages of 3rd and 4th order Higher Order Statistics (HOS) to priorities the common signals during the channel estimation. In this paper, we present the detailed design and evaluation of HICA blind channel estimation method. We showed the simulation results of HICA against the state-of-art techniques for channel estimation using BER, MSE, and PAPR.
KED-AES algorithm: combined key encryption decryption and advance encryption standard algorithm
Authors: Arboleda Edwin Romeroso , Fenomeno Carla Eunice R. , Jimenez Joshua Z.
Published: March 2020

Two existing cryptosystems are being combined and proposed. It is the enhanced combination of KED (Key Encryption Decryption), a cryptosystem that uses modulo 69 and the AES (Advance Encryption Standard) cryptography. The strength of the KED is that the keys are being used by the sender and the receiving end. The AES is easy to implement and has good defense against various attacks such as hacking.
Solar irradiance forecasting using fuzzy logic and multilinear regression approach: A case study of Punjab, India
Authors: Mehta Sahil , Basak Prasenjit
Published: March 2020

The accurate forecasting of solar irradiance depends on various uncertain parameters like time of day, temperature, wind speed, humidity, and atmospheric pressure. All these play an important role in calculating PV power output. In this paper, a novel approach for forecasting of solar irradiance using flexible and accurate fuzzy logic and robust multi-linear regression approach has been proposed considering the above mentioned five variables. Based on the simultaneous consideration of those five variables, the solar irradiance is forecasted using the proposed methodology at a particular location in India, and the results are compared with the real time measured value of solar irradiance at that location on the days for which solar irradiance are forecasted. The proposed method is validated by comparing the results with real time data. The error analysis of the fuzzy logic based proposed system shows the root mean square error of 10.011 and mean absolute percentage error of 1.703%, while compared with real time data measured by instruments pyranometer, anemometer etc. The same results are found better while compared with the results obtained using multilinear regression approach.
A model free dissolved oxygen controller for industry effluent using hybrid variables measuring technique
Authors: Stanley P. Kingston , A. Sanjeevi Gandhi , Chandy D. Abraham
Published: March 2020

The present scenario of the world relays on water scarcity, enormous amount of water is needed for people but the world has pollution which makes a great effect. Water is polluted due to various reasons such as industrial waste, sewage, and global warming and oil pollution and mainly polluted due to industrial effluent waste water. The main objective of this paper is to control the dissolved oxygen of the industrial waste water by measuring turbidity and dissolved oxygen (DO). Turbidity is measured through the intensity of the light through the medium in Nephelometric unit (NTU) and dissolved oxygen is measured in PPM through amperometic electrode method. The controller is designed to improve the quality of the effluent water through the aeration process. The very low concentration of dissolved oxygen (DO) level is too harmful to the aquatic ecosystem and it pollutes the water to the maximum extent. This measurement method of turbidity has an enhanced idea which processed with the software and it is monitored. The controller is designed as such with the condition of inverse proportionality of water turbidity and dissolved oxygen, which contributes an additive advantage to the concept design.
Subsynchronous resonance oscillations mitigation via fuzzy controlled novel braking resistor model
Authors: Fayez Mohamed , Mandour M. , El-Hadidy M. , Bendary F.
Published: March 2020

Subsynchronous resonance (SSR) torsional torque oscillations is a problem of a great concern in the power engineering community. SSR causes torsional torque oscillations with ever-increasing magnitudes occurring in the machine shaft sections causing a premature fatigue life expenditure of the shaft metal. In this paper, dynamic braking switching strategy designed through fuzzy logic control theory and implemented via novel braking resistor model, namely chopper rectifier controlled braking resistor for tempering SSR torsional torque oscillations of a large turbo-generator. The proposed mitigation scheme has been tested on the IEEE second benchmark model for SSR studies. Comparative simulation study via MATLAB/Simulink-based modeling and simulation environment of the test model with and without the suggested mitigation regime should demonstrate its effectuality for mitigation of SSR torsional torque oscillations.
Improved speed response of DC motor via intelligent techniques
Authors: Rashag Hassan Farahan
Published: March 2020

The classical Proportional- Integral (PI) control for Direct Current (DC) motor causes slow response of actual speed with high overshoot and undershoot which leads to sluggishness of the system. To minimize the problem of PI controller, intelligent technique based on hybrid neural network sliding mode control NN-SMC is suggested.  The benefits of SMC are that it is simple, and tough to parameter deviations as compared with other controllers. In this paper, the neural network NN is used to minimize the error between reference speed and actual speed. In addition, the SMC aim is to control and optimize the voltage that is supplies the DC motor which guarantees the robust performance of the speed controller under disturbances. The proposed method for the speed control is first calculated and executed to DC motor by using MATLAB SIMULINK. The results of the suggested NN-SMC are compared with the traditional PI controller. The results obviously show the supremacy of NN-SMC over PI controller.
Optimization of transmission signal by artificial intelligent
Authors: Rashag Hassan Farahan , Ali Mohammed H.
Published: March 2020

In this method, radial basis function network RBFNN is an artificial intelligent which is used to identify and classify the communication system performance.  RBFNN is one type of neural network which has activation functions. It consists of three layer input layer, hidden layer and output linear combination. One of the main problems of communication system is that it causes slow response for sending signal via the transmission devices. Therefore, the artificial intelligent by RBFNN is used to optimize the transmission signal. The input signal is trained and testing by neurons with weight and this lead to provide linear output. The simulation results have the optimization specifics over the traditional communication transmission devices.
An immune memory and negative selection to visualizing clinical pathways from electronic health record data
Authors: Berquedich Mouna , Kamach Oulaid , Masmoudi Malek , Deshayes Laurent
Published: March 2020

Clinical pathways indicate the applicable treatment order of interventions. In this paper we propose a data-driven methodology to extract common clinical pathways from patient-centric Electronic Health Record data (EHR). The analysis of patient's, can lead to better regarding pathologies. The proposed algorithmic methodology consists to designing a system of control and analysis of patient records based on an analogy between the elements of the new EHRs and the biological immune systems. The detection of patient profiles ensured by biclustering Matrix. We rely on biological immunity to develop a set of models for structuring knowledge extracted from EHR and to make pathway analysis decisions. A specific analysis of the functional data leds to the detection of several types of patients who share the same EHR information. This methodology demonstrates its ability to simultaneously processing data, and is able to providing information for understanding and identifying the path of patients as well as predicting the path of future patients.
Fotografia e escrita
Authors: Brandini Laura Taddei
Published: March 2020

A proposta deste artigo é fazer uma releitura da Câmara clara(1980), de Roland Barthes, tendo em vista a teia de relações que essa obra cria ligando a fotografia, a escrita e o luto. Para tanto, na esteira de numerosos críticos, defendo sua compreensão não como um texto teórico, mas literário, em que o escritor expõe o caminho reflexivo que percorre para tentar reencontrar sua mãe, morta. O diferencial deste texto com relação à fortuna crítica sobre esse, que foi o último livro que Barthes publicou em vida, reside em evidenciar como da contemplação da fotografia o escritor passa à escrita da mesma, que é a escrita do « nada a dizer ». Nesse processo, o tempo, enquanto elemento da narrativa, tem papel fundamental, como minhas análises do texto barthesiano demonstrarão.
Chapeuzinho Vermelho
Authors: Alcantara Valquiria Pereira
Published: March 2020

Quentin Blake ilustrou vários trabalhos de Roald Dahl possibilitando um diálogo instigante entre texto verbal e imagens. Apresentamos uma proposta de análise de “Chapeuzinho Vermelho e o lobo” e “Os três porquinhos” buscando a melhor compreensão de como o texto dahliano e as ilustrações de Blake se articulam à luz do percurso sugerido por Sophie Van der Linden detendo-nos, principalmente, nas relações e funções estabelecidas entre os textos verbal e visual. Observamos as vinhetas e as ilustrações que ocupam página inteira e como as imagens relacionam-se com o texto em língua inglesa bem como as traduções publicadas no Brasil e em Portugal. Como resultado de nossa análise verificamos que as ilustrações de Blake mantêm relação dinâmica com o texto verbal ora repetindo, ora ampliando o sentido do texto além de contribuir para a atualização dos contos proporcionando uma experiência bem-humorada de fruição dos textos. Concluímos que, embora o diálogo entre as ilustrações de Quentin Blake e o texto de Dahl se dê de forma diversa no que tange a língua, os leitores podem ter uma experiência rica e estimulante.
“Estetização da política” e “politização da arte” na URSS
Authors: Villela Thyago Marão
Published: March 2020

O artigo objetiva analisar as relações históricas e conceituais entre Walter Benjamin e o movimento produtivista soviético, centrando-se, sobretudo, na relação entre a noção de “politização da arte”, defendida por Benjamin como dispositivo de combate ao fascismo no ensaio “A obra de arte na época de sua reprodutibilidade técnica”, de 1936, e a noção de “factografia”, desenvolvida pelo produtivista soviético Sergei Tretiakov a partir de 1927. Sustenta-se, neste texto, que as categorias de “estetização da política” e de “politização da arte” tiveram seu primeiro desenvolvimento conceitual no pensamento de Benjamin a partir de sua viagem à URSS (1926-1927) e do seu contato com o pensamento produtivista.
Barricadas em rodapés de jornais
Authors: Ramos Ana Flavia Cernic
Published: March 2020

Em abril de 1880, a Gazeta de Noticias deu início à publicação d’O livro verde, do húngaro Mór Jokai. Repleto de movimentos conspiratórios, o romance-folhetim contava a história da “Insurreição Dezembrista”, ocorrida na Rússia em 1825 contra a coroação do czar Nicolau I, tematizando os riscos das grandes agitações sociais. Em meio aos ecos do “Motim do Vintém”, o romance chegava ao Brasil num momento de intensas disputas políticas acerca de uma nova reforma eleitoral. Em diálogo com as notícias internacionais sobre os atentados ao czar Alexandre II e a anistia concedida na França aos integrantes da Comuna de Paris, a proposta deste artigo é mostrar como a escolha do folhetim de Jokai serviu para pautar temas caros à intelectualidade brasileira naquele final de século, tais como o dilema entre reforma e revolução. Pretende-se realizar uma análise que enfatize tanto a articulação do folhetim com outros conteúdos do jornal quanto o uso da literatura como espaço de intervenção social e política.
A Winged Word on Marriage
Authors: Lin Lijuan
Published: March 2020

A foreign saying on marriage became widely known in China through Qian Zhongshu’s 1947 novel Fortress Besieged. As the novelist tells us, this saying has its source in both English and French literature, and in its different versions, marriage is either likened to a besieged fortress or a bird cage. This paper examines the origin and transmission of the saying in Greek, Arabic and Syriac sources, and argues that this saying originated in the so-called literature of the Christianized Socratic-Cynic philosophy, which once flourished in Syria. It became popular in the Byzantine and Arabic world after having been included into several famous Greek and Arabic gnomologies. Then it was introduced into modern languages, developed into different versions, finally came to China and became a household word among Chinese people.
The Role of North Korea in China’s Civil War: The Soviet-led North Korean Assistance to the CPC in the Northeast Theater, 1946-1948
Authors: Nisimov Tomer
Published: March 2020

Previous studies of China’s civil war have concentrated on different aspects and causes leading to the Communist victory and focused on political, economic, and military explanations. Few studies, however, have examined the features of foreign intervention and assistance to the Communist Party of China and their contribution to the latter’s success. Sino-Soviet relations and cooperation during the war have received the attention of several studies, but the role of North Korea in the war has remained obscure. As information regarding North Korea’s actions during China’s civil war remains largely inaccessible, few studies have debated the question of whether North Korea had ever deployed its forces in China’s Northeast in order to assist their Chinese comrades. Relying on military and intelligence documents from the Republic of China, this article shows how by the time of the Soviet withdrawal from China’s Northeast, the USSR had become resolute about turning North Korea into a militarized state in order to protect its own interests in the region and assist the Chinese Communists.
Integrative taxonomic and geographic variation analyses in Cyrtodactylus aequalis (Squamata: Gekkonidae) from southern Myanmar (Burma): one species, two different stories
Authors: Lee Grismer L. , Perry L. Wood , Grismer Marta S. , Quah Evan S.H. , Thura Myint Kyaw , Oaks Jamie R. , Lin Aung , Lim Diana Y.
Published: March 2020

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain non-monophyletic lineages. This is especially true at the species level where small amounts of gene flow may not preclude the evolution of localized adaptions in different geographic areas while underpinning the paraphyletic nature of each population with respect to the other. We illustrate this point by examining genetic and morphological variation among three putatively allopatric populations of the granite-dwelling Bent-toed Gecko Cyrtodactylus aequalis from hilly regions in southeastern Myanmar. In the absence of molecular phylogenetic inference, a compelling argument for three morphologically diagnosable species could be marshaled. However, when basing the morphological analyses of geographic variation on a molecular phylogeny, there is a more compelling argument that only one species should be recognized. We are cognizant of the fact however, that when dealing with rare species or specimens for which no molecular data are possible, judicious morphological analyses are the only option—and the desired option given the current worldwide biodiversity crisis.
Mountain endemism in Malesian geckos: can biotic interactions push lizards up hills?
Authors: Oliver Paul M. , Brown Rafe M. , Karin Benjamin R. , Lee Grismer L.
Published: March 2020

Historical and contemporary processes shaping striking variation in terrestrial biodiversity along elevational gradients have received much attention from evolutionary biologists, often by way of comparisons to latitudinal environmental gradients. Here we synthetically review what is known of the diversity and origin of upland endemic geckos across the Malesian region (south-east Asia and Melanesia). Approximately 20% of the regional gecko fauna is endemic to mountains, but only around 8% have distributions centred on what we consider true montane habitats over 1000 metres above sea level. A majority of upland lineages lack close relatives in surrounding lowlands (although there are many exceptions) and some are highly phylogenetically divergent (e.g., estimated divergence from all other gecko taxa dating to the mid-Miocene or earlier). In several cases upland radiations are allied to other taxa centred on small islands or in disturbed lowland habitats, but absent or exceptionally rare in most lowland rainforest areas. A number of other upland lineages may have originated on smaller islands that are now merged into larger landmasses such as Sumatra and New Guinea. Based on often deep phylogenetic divergences, low community diversity and disjunct distributions across uplands and islands, we suggest that at least some upland lineages are more limited by biotic interactions than they are by climate. As global climates continue to warm in coming decades, such taxa may be particularly affected by upslope shifts of competitors and predators from lower elevations.
Processes Controlling Sea Surface Temperature Variability of Ningaloo Niño
Authors: Guo Yaru , Li Yuanlong , Wang Fan , Wei Yuntao , Rong Zengrui
Published: March 2020

A high-resolution (3–8 km) regional oceanic general circulation model is utilized to understand the sea surface temperature (SST) variability of Ningaloo Niño in the southeast Indian Ocean (SEIO). The model reproduces eight Ningaloo Niño events with good fidelity and reveals complicated spatial structures. Mesoscale noises are seen in the warming signature and confirmed by satellite microwave SST data. Model experiments are carried out to quantitatively evaluate the effects of key processes. The results reveal that the surface turbulent heat flux (primarily latent heat flux) is the most important process (contribution > 68%) in driving and damping the SST warming for most events, while the roles of the Indonesian Throughflow (~15%) and local wind forcing are secondary. A suitable air temperature warming is essential to reproducing the reduced surface latent heat loss during the growth of SST warming (~66%), whereas the effect of the increased air humidity is negligibly small (1%). The established SST warming in the mature phase causes increased latent heat loss that initiates the decay of warming. A 20-member ensemble simulation is performed for the 2010/11 super Ningaloo Niño, which confirms the strong influence of ocean internal processes in the redistribution of SST warming signatures. Oceanic eddies can dramatically modulate the magnitudes of local SST warming, particularly in offshore areas where the “signal-to-noise” ratio is low, raising a caution for evaluating the predictability of Ningaloo Niño and its environmental consequences.
Rainfall and DSD Parameters Comparison between Micro Rain Radar, Two-Dimensional Video and Parsivel2 Disdrometers, and S-Band Dual-Polarization Radar
Authors: Adirosi Elisa , Baldini Luca , Tokay Ali
Published: March 2020

A well-designed deployment of well-maintained surface instruments as well as abundant rainfall provided an excellent dataset with which to evaluate the Micro Rain Radar (MRR) performance for estimating raindrop size distribution (DSD) and its integral rainfall parameters with respect to the consolidated devices during the Iowa Flood Studies (IFloodS) field campaign. The MRR was collocated with two-dimensional video disdrometer (2DVD) and Autonomous Parsivel2 Unit (APU) at three different sites located at 5–70-km distances from the National Aeronautics and Space Administration’s S-band dual-polarization Doppler radar (NPOL). A comparative study between MRR, 2DVD, APU, and NPOL was conducted including all rainy minutes as well as minutes of stratiform rain and convective rain. Considering 2DVD as a primary reference, a good agreement was evident for reflectivity between MRR’s lowest reliable height and 2DVD with an absolute bias of less than 2 dB even in convective rain except for one site. For rainfall rate, the percent absolute bias between MRR and 2DVD ranged between 25% and 35% in stratiform rain and about 10% higher in convective rain. Agreement for mean mass-weighted raindrop diameter was good (bias less than 0.1 mm), whereas MRR overestimated the normalized intercept parameter of the gamma DSD [mean bias among the three sites was −0.13 log(mm−1 m−3)]. The agreement between MRR and APU was slightly worse than the one between MRR and 2DVD. When the horizontal and differential reflectivities of NPOL were compared with the ones derived from the MRR DSD resampled within the radar volume, we found an absolute bias of approximately 3 and 0.4 dB, respectively.
Assimilation of GOES-16 Radiances and Retrievals into the Warn-on-Forecast System
Authors: Jones Thomas A. , Skinner Patrick , Yussouf Nusrat , Knopfmeier Kent , Reinhart Anthony , Wang Xuguang , Bedka Kristopher , Smith William , Palikonda Rabindra
Published: March 2020

The increasing maturity of the Warn-on-Forecast System (WoFS) coupled with the now operational GOES-16 satellite allows for the first time a comprehensive analysis of the relative impacts of assimilating GOES-16 all-sky 6.2-, 6.9-, and 7.3-μm channel radiances compared to other radar and satellite observations. The WoFS relies on cloud property retrievals such as cloud water path, which have been proven to increase forecast skill compared to only assimilating radar data and other conventional observations. The impacts of assimilating clear-sky radiances have also been explored and shown to provide useful information on midtropospheric moisture content in the near-storm environment. Assimilation of all-sky radiances adds a layer of complexity and is tested to determine its effectiveness across four events occurring in the spring and summer of 2019. Qualitative and object-based verification of severe weather and the near-storm environment are used to assess the impact of assimilating all-sky radiances compared to the current model configuration. We focus our study through the entire WoFS analysis and forecasting cycle (1900–0600 UTC, daily) so that the impacts throughout the evolution of convection from initiation to large upscale growth can be assessed. Overall, assimilating satellite data improves forecasts relative to radar-only assimilation experiments. The retrieval method with clear-sky radiances performs best overall, but assimilating all-sky radiances does have very positive impacts in certain conditions. In particular, all-sky radiance assimilation improved convective initiation forecast of severe storms in several instances. This work represents an initial attempt at assimilating all-sky radiances into the WoFS and additional research is ongoing to further improve forecast skill.
Making Room at the Bedside
Authors: Wickersham Alexis , Zavodnick Jillian , Thum Andrew , Robertson Bonnie , Ackermann Lily
Published: March 2020

Interdisciplinary rounding has been shown to improve patient safety and provider engagement. Many models for interdisciplinary rounding have been proposed but few focus on preserving bedside medical education. The authors changed the interdisciplinary bedside rounding model to accommodate more time for medical education. The objective was to assess perceptions of communication, care coordination, and teamwork surrounding this change. Resident and attending physicians and unit-based nursing staff completed an anonymous online survey prior to and following the rounding intervention. Length of stay on medical units also was monitored prior to and following the rounding intervention. Following the intervention, there were perceived improvements in interdisciplinary communication, care coordination, and teamwork, and there were no significant changes in length of stay.
“He Should Learn That He Cannot Get a Woman for Free”: Male Elopers and Constructions of Masculinity in the Afghan Justice System
Authors: Wimpelmann Torunn , Hakimi Aziz , Saadat Masooma
Published: March 2020

This article explores constructions of gender, masculinity, and class in moral crimes prosecutions, and their legal aftermaths in Afghanistan. It argues that the lack of attention to men in advocacy and research about moral crimes, while reflecting a (geo-) politicized conflation of gender with women, constitute both an empirical and an analytical oversight. The first part of the article discusses the legal grounds for the prosecution of men for “moral crimes” in Afghanistan and presents statistical data that reveals large-scale incarceration of men for pursuing consensual, heterosexual relations, including the non-codified crime of elopement. In the second part, we use ethnographic data to probe into the ways in which the treatment of male elopers is based on specific notions of gender, sexuality, and masculinity. We suggest that the interrelated, yet differentiated, prosecution of male and female elopers in Afghanistan can be usefully understood in terms of a gender regime that places different expectations on men and women. Women’s gender performance is ranked according to (verifiable) chastity, men’s gender performance according to the (legitimate, i.e., honorable) command of resources.
Tin and Oxygen-Vacancy Co-doping into Hematite Photoanode for Improved Photoelectrochemical Performances
Authors: Xiao Chenhong , Zhou Zhongyuan , Li Liujing , Wu Shaolong , Li Xiaofeng
Published: March 2020

Hematite (α-Fe2O3) material is regarded as a promising candidate for solar-driven water splitting because of the low cost, chemical stability, and appropriate bandgap; however, the corresponding system performances are limited by the poor electrical conductivity, short diffusion length of minority carrier, and sluggish oxygen evolution reaction. Here, we introduce the in situ Sn doping into the nanoworm-like α-Fe2O3 film with ultrasonic spray pyrolysis method. We show that the current density at 1.23 V vs. RHE (Jph@1.23V) under one-sun illumination can be improved from 10 to 130 μA/cm2 after optimizing the Sn dopant density. Moreover, Jph@1.23V can be further enhanced 25-folds compared to the untreated counterpart via the post-rapid thermal process (RTP), which is used to introduce the defect doping of oxygen vacancy. Photoelectrochemical impedance spectrum and Mott-Schottky analysis indicate that the performance improvement can be ascribed to the increased carrier density and the decreased resistances for the charge trapping on the surface states and the surface charge transferring into the electrolyte. X-ray photoelectron spectrum and X-ray diffraction confirm the existence of Sn and oxygen vacancy, and the potential influences of varying levels of Sn doping and oxygen vacancy are discussed. Our work points out one universal approach to efficiently improve the photoelectrochemical performances of the metal oxide semiconductors.
Family reunion via error correction: an efficient analysis of duplex sequencing data
Authors: Stoler Nicholas , Arbeithuber Barbara , Povysil Gundula , Heinzl Monika , Salazar Renato , Makova Kateryna D , Tiemann-Boege Irene , Nekrutenko Anton
Published: March 2020

Background

Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original DNA molecules, which allows distinguishing true nucleotide substitutions from PCR amplification and sequencing artifacts. This strategy comes at a cost—sequencing the same molecule multiple times increases dynamic range but significantly diminishes coverage, making whole genome duplex sequencing prohibitively expensive. Furthermore, every duplex experiment produces a substantial proportion of singleton reads that cannot be used in the analysis and are thrown away.

Results

In this paper we demonstrate that a significant fraction of these reads contains PCR or sequencing errors within duplex tags. Correction of such errors allows “reuniting” these reads with their respective families increasing the output of the method and making it more cost effective.

Conclusions

We combine an error correction strategy with a number of algorithmic improvements in a new version of the duplex analysis software, Du Novo 2.0. It is written in Python, C, AWK, and Bash. It is open source and readily available through Galaxy, Bioconda, and Github: https://github.com/galaxyproject/dunovo.
Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress
Authors: Arisha Mohamed Hamed , Aboelnasr Hesham , Ahmad Muhammad Qadir , Liu Yaju , Tang Wei , Gao Runfei , Yan Hui , Kou Meng , Wang Xin , Zhang Yungang , Li Qiang
Published: March 2020

Background

Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt stress is seriously limiting its production and distribution. Due to lacking of reference genome, transcriptome sequencing is offering a rapid approach for crop improvement with promising agronomic traits and stress adaptability.

Results

Five cDNA libraries were prepared from the third true leaf of hexaploid sweetpotato at seedlings stage (Xuzi-8 cultivar) treated with 200 mM NaCl for 0, 1, 6, 12, 48 h. Using second and third generation technology, Illumina sequencing generated 170,344,392 clean high-quality long reads that were assembled into 15,998 unigenes with an average length 2178 base pair and 96.55% of these unigenes were functionally annotated in the NR protein database. A number of 537 unigenes failed to hit any homologs which may be considered as novel genes. The current results indicated that sweetpotato plants behavior during the first hour of salt stress was different than the other three time points. Furthermore, expression profiling analysis identified 4, 479, 281, 508 significantly expressed unigenes in salt stress treated samples at the different time points including 1, 6, 12, 48 h, respectively as compared to control. In addition, there were 4, 1202, 764 and 2195 transcription factors differentially regulated DEGs by salt stress at different time points including 1, 6, 12, 48 h of salt stress. Validation experiment was done using 6 randomly selected unigenes and the results was in agree with the DEG results. Protein kinases include many genes which were found to play a vital role in phosphorylation process and act as a signal transductor/ receptor proteins in membranes. These findings suggest that salt stress tolerance in hexaploid sweetpotato plants may be mainly affected by TFs, PKs, Protein Detox and hormones related genes which contribute to enhance salt tolerance.

Conclusion

These transcriptome sequencing data of hexaploid sweetpotato under salt stress conditions can provide a valuable resource for sweetpotato breeding research and focus on novel insights into hexaploid sweetpotato responses to salt stress. In addition, it offers new candidate genes or markers that can be used as a guide to the future studies attempting to breed salt tolerance sweetpotato cultivars.
Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)
Authors: Bernard Anthony , Marrano Annarita , Donkpegan Armel , Brown Patrick J. , Leslie Charles A. , Neale David B. , Lheureux Fabrice , Dirlewanger Elisabeth
Published: March 2020

Background

Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™J. regia700 K SNP array, with phenological data from 2018, 2019 and legacy data. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F1progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection.

Results

Using GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date.

Conclusions

This study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, one of the most important traits for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.
Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication
Authors: Amiri Ghanatsaman Zeinab , Wang Guo-Dong , Asadollahpour Nanaei Hojjat , Asadi Fozi Masood , Peng Min-Sheng , Esmailizadeh Ali , Zhang Ya-Ping
Published: March 2020

Background

Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported.

Results

Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3′-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work.

Conclusions

Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)
Authors: Han Guohao , Liu Shiyu , Jin Yuli , Jia Mengshu , Ma Pengtao , Liu Hong , Wang Jing , An Diaoguo
Published: March 2020

Background

Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will facilitate the transfer and utilization of elite genes derived from rye in wheat breeding.

Results

In the present study, five rye cultivars including Imperial, German White, Jingzhouheimai, Baili and Guyuan were sequenced by specific-locus amplified fragment sequencing (SLAF-seq) to develop large-scale rye-specific markers. Based on SLAF-seq and bioinformatics analyses, a total of 404 universal PCR-based and a whole set of Kompetitive allele-specific PCR (KASP) markers specific for the 14 individual rye chromosome arms were developed and validated. Additionally, two KASP markers specific for 1RS and 2RL were successfully applied in the detection of 1RS translocations in a natural population and 2RL chromosome arms in wheat-rye derived progenies that conferred adult resistance to powdery mildew.

Conclusion

The 404 PCR-based markers and 14 KASP markers specific for the 14 individual rye chromosome arms developed in this study can enrich the marker densities for gene mapping and accelerate the utilization of rye-derived genes in wheat improvement. Especially, the KASP markers achieved high-throughput and accurate detection of rye chromatin in wheat background, thus can be efficiently used in marker-assisted selection (MAS). Besides, the strategy of rye-specific PCR-based markers converting into KASP markers was high-efficient and low-cost, which will facilitate the tracing of alien genes, and can also be referred for other wheat relatives.
Genome-wide analysis of MicroRNA-messenger RNA interactome in ex-vivo gill filaments, Anguilla japonica
Authors: Ng Hoi Man , Ho Jeff Cheuk Hin , Nong Wenyan , Hui Jerome Ho Lam , Lai Keng Po , Wong Chris Kong Chu
Published: March 2020

Background

Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-establishment of fluid and electrolyte homeostasis. The osmoregulatory plasticity of gills provides an excellent model to study the role of microRNAs (miRs) in adaptive osmotic responses. The present study is to characterize an ex-vivo gill filament culture and using omics approach, to decipher the interaction between tonicity-responsive miRs and gene targets, in orchestrating the osmotic stress-induced responses.

Results

Ex-vivo gill filament culture was exposed to Leibovitz’s L-15 medium (300 mOsmol l− 1) or the medium with an adjusted osmolality of 600 mOsmol l− 1for 4, 8 and 24 h. Hypertonic responsive genes, including osmotic stress transcriptional factor, Na+/Cl−-taurine transporter, Na+/H+exchange regulatory cofactor, cystic fibrosis transmembrane regulator, inward rectifying K+channel, Na+/K+-ATPase, and calcium-transporting ATPase were significantly upregulated, while the hypo-osmotic gene, V-type proton ATPase was downregulated. The data illustrated that the ex-vivo gill filament culture exhibited distinctive responses to hyperosmotic challenge. In the hyperosmotic treatment, four key factors (i.e. drosha RNase III endonuclease, exportin-5, dicer ribonuclease III and argonaute-2) involved in miR biogenesis were dysregulated (P < 0.05). Transcriptome and miR-sequencing of gill filament samples at 4 and 8 h were conducted and two downregulated miRs, miR-29b-3p and miR-200b-3p were identified. An inhibition of miR-29b-3p and miR-200b-3p in primary gill cell culture led to an upregulation of 100 and 93 gene transcripts, respectively. Commonly upregulated gene transcripts from the hyperosmotic experiments and miR-inhibition studies, were overlaid, in which two miR-29b-3p target-genes [Krueppel-like factor 4 (klf4), Homeobox protein Meis2] and one miR-200b-3p target-gene (slc17a5) were identified. Integrated miR-mRNA-omics analysis revealed the specific binding of miR-29b-3p on Klf4 and miR-200b-3p on slc17a5. The target-genes are known to regulate differentiation of gill ionocytes and cellular osmolality.

Conclusions

In this study, we have characterized the hypo-osmoregulatory responses and unraveled the modulation of miR-biogenesis factors/the dysregulation of miRs, using ex-vivo gill filament culture. MicroRNA-messenger RNA interactome analysis of miR-29b-3p and miR-200b-3p revealed the gene targets are essential for osmotic stress responses.
Assembling and validating a heart failure-free cohort from the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study
Authors: Goyal Parag , Mefford Matthew T. , Chen Ligong , Sterling Madeline R. , Durant Raegan W. , Safford Monika M. , Levitan Emily B.
Published: March 2020

Background

Studies examining incident heart failure (HF) have been limited to select populations. To examine incident HF with broader generalizability, there is need to assemble a HF-free cohort using a geographically-diverse sample. We aimed to develop and validate a simple medication-based strategy for assembling a HF-free cohort from the REasons for Geographic And Racial Differences in Stroke (REGARDS) study.

Methods

We examined REGARDS participants with ≥6 months of Medicare inpatient and outpatient claims data at the time of the baseline in-home study examination. To assemble a HF-free cohort, we identified and excluded participants taking HF-specific medications. To validate this approach, we evaluated event rates among this cohort and assessed diagnostic performance using Medicare claims-based definitions of HF as the referent standard.

Results

Among 28,884 eligible participants, 3125 were excluded from the proposed HF-free cohort, leaving a total of 25,759 (89%) participants. Depending on the Medicare definition used as the referent, the negative predictive value of this approach ranged from 95.0–99.2%. Negative predictive value was stable across age, sex, and race strata.

Conclusions

The approach to assemble a HF-free cohort in REGARDS can serve as the basis for future studies to examine incident HF in REGARDS and similar studies.
Serum 25-Hydroxyvitamin D and the risk of mortality in adult patients with Sepsis: a meta-analysis
Authors: Li Yuye , Ding Shifang
Published: March 2020

Background

Vitamin D deficiency has been related to the risk of sepsis. However, previous studies showed inconsistent results regarding the association between serum 25-hydroxyvitamin D (25 (OH) D) and mortality risk in septic patients. We aimed to evaluate the relationship between serum 25 (OH) D at admission and mortality risk in adult patients in a meta-analysis.

Methods

Follow-up studies that provided data of multivariate adjusted relative risk (RR) between serum 25 (OH) D and mortality risk in septic patients were retrieved via systematic search of PubMed and Embase databases. A random effect model was used to pool the results.

Results

Eight studies with 1736 patients were included. Results of overall meta-analysis showed that lower 25 (OH) D at admission was independently associated with increased risk or mortality (adjusted RR: 1.93, p < 0.001; I2 = 63%) in patients with sepsis. Exploring subgroup association showed that patients with severe vitamin D deficiency (25 (OH) D < 10 ng/ml) was significantly associated with higher mortality risk (adjusted RR: 1.92, p < 0.001), but the associations were not significant for vitamin D insufficiency (25 (OH) D 20~30 ng/ml) or deficiency (25 (OH) D 10~20 ng/ml). Further analyses showed that the association between lower serum 25 (OH) D and higher mortality risk were consistent in studies applied different diagnostic criteria for sepsis (systemic inflammatory response syndrome, Sepsis-2.0, or Sepsis-3.0), short-term (within 1 month) and long-term studies (3~12 months), and in prospective and retrospective studies.

Conclusions

Severe vitamin D deficiency may be independently associated with increased mortality in adult patients with sepsis. Large-scale prospective studies are needed to validate our findings.
Explaining age disparities in tuberculosis burden in Taiwan: a modelling study
Authors: Fu Han , Lin Hsien-Ho , Hallett Timothy B. , Arinaminpathy Nimalan
Published: March 2020

Background

Tuberculosis (TB) burden shows wide disparities across ages in Taiwan. In 2016, the age-specific notification rate in those older than 65 years old was about 100 times as much as in those younger than 15 years old (185.0 vs 1.6 per 100,000 population). Similar patterns are observed in other intermediate TB burden settings. However, driving mechanisms for such age disparities are not clear and may have importance for TB control efforts.

Methods

We hypothesised three mechanisms for the age disparity in TB burden: (i) older age groups bear a higher risk of TB progression due to immune senescence, (ii) elderly cases acquired TB infection during a past period of high transmission, which has since rapidly declined and thus contributes to little recent infections, and (iii) assortative mixing by age allows elders to maintain a higher risk of TB infection, while limiting spillover transmission to younger age groups. We developed a series of dynamic compartmental models to incorporate these mechanisms, individually and in combination. The models were calibrated to the TB notification rates in Taiwan over 1997–2016 and evaluated by goodness-of-fit to the age disparities and the temporal trend in the TB burden, as well as the deviance information criterion (DIC). According to the model performance, we compared contributions of the hypothesised mechanisms.

Results

The ‘full’ model including all the three hypothesised mechanisms best captured the age disparities and temporal trend of the TB notification rates. However, dropping individual mechanisms from the full model in turn, we found that excluding the mechanism of assortative mixing yielded the least change in goodness-of-fit. In terms of their influence on the TB dynamics, the major contribution of the ‘immune senescence’ and ‘assortative mixing’ mechanisms was to create disparate burden among age groups, while the ‘declining transmission’ mechanism served to capture the temporal trend of notification rates.

Conclusions

In settings such as Taiwan, the current TB burden in the elderly may be impacted more by prevention of active disease following latent infection, than by case-finding for blocking transmission. Further studies on these mechanisms are needed to disentangle their impacts on the TB epidemic and develop corresponding control strategies.