Recognition of motor imagery electroencephalogram based on flicker noise spectroscopy and weighted filter bank common spatial pattern / 生物医学工程学杂志

Due to the high complexity and subject variability of motor imagery electroencephalogram, its decoding is limited by the inadequate accuracy of traditional recognition models. To resolve this problem, a recognition model for motor imagery electroencephalogram based on flicker noise spectrum (FNS) and weighted filter bank common spatial pattern ( wFBCSP) was proposed. First, the FNS method was used to analyze the motor imagery electroencephalogram. Using the second derivative moment as structure function, the ensued precursor time series were generated by using a sliding window strategy, so that hidden dynamic information of transition phase could be captured. Then, based on the characteristic of signal frequency band, the feature of the transition phase precursor time series and reaction phase series were extracted by wFBCSP, generating features representing relevant transition and reaction phase. To make the selected features adapt to subject variability and realize better generalization, algorithm of minimum redundancy maximum relevance was further used to select features. Finally, support vector machine as the classifier was used for the classification. In the motor imagery electroencephalogram recognition, the method proposed in this study yielded an average accuracy of 86.34%, which is higher than the comparison methods. Thus, our proposed method provides a new idea for decoding motor imagery electroencephalogram.

Multi-task motor imagery electroencephalogram classification based on adaptive time-frequency common spatial pattern combined with convolutional neural network / 生物医学工程学杂志

The effective classification of multi-task motor imagery electroencephalogram (EEG) is helpful to achieve accurate multi-dimensional human-computer interaction, and the high frequency domain specificity between subjects can improve the classification accuracy and robustness. Therefore, this paper proposed a multi-task EEG signal classification method based on adaptive time-frequency common spatial pattern (CSP) combined with convolutional neural network (CNN). The characteristics of subjects' personalized rhythm were extracted by adaptive spectrum awareness, and the spatial characteristics were calculated by using the one-versus-rest CSP, and then the composite time-domain characteristics were characterized to construct the spatial-temporal frequency multi-level fusion features. Finally, the CNN was used to perform high-precision and high-robust four-task classification. The algorithm in this paper was verified by the self-test dataset containing 10 subjects (33 ± 3 years old, inexperienced) and the dataset of the 4th 2018 Brain-Computer Interface Competition (BCI competition Ⅳ-2a). The average accuracy of the proposed algorithm for the four-task classification reached 93.96% and 84.04%, respectively. Compared with other advanced algorithms, the average classification accuracy of the proposed algorithm was significantly improved, and the accuracy range error between subjects was significantly reduced in the public dataset. The results show that the proposed algorithm has good performance in multi-task classification, and can effectively improve the classification accuracy and robustness.

Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data / 基因组蛋白质组与生物信息学报·英文版

In this work, we describe the development of Polar Gini Curve, a method for characterizing cluster markers by analyzing single-cell RNA sequencing (scRNA-seq) data. Polar Gini Curve combines the gene expression and the 2D coordinates ("spatial") information to detect patterns of uniformity in any clustered cells from scRNA-seq data. We demonstrate that Polar Gini Curve can help users characterize the shape and density distribution of cells in a particular cluster, which can be generated during routine scRNA-seq data analysis. To quantify the extent to which a gene is uniformly distributed in a cell cluster space, we combine two polar Gini curves (PGCs)-one drawn upon the cell-points expressing the gene (the "foreground curve") and the other drawn upon all cell-points in the cluster (the "background curve"). We show that genes with highly dissimilar foreground and background curves tend not to uniformly distributed in the cell cluster-thus having spatially divergent gene expression patterns within the cluster. Genes with similar foreground and background curves tend to uniformly distributed in the cell cluster-thus having uniform gene expression patterns within the cluster. Such quantitative attributes of PGCs can be applied to sensitively discover biomarkers across clusters from scRNA-seq data. We demonstrate the performance of the Polar Gini Curve framework in several simulation case studies. Using this framework to analyze a real-world neonatal mouse heart cell dataset, the detected biomarkers may characterize novel subtypes of cardiac muscle cells. The source code and data for Polar Gini Curve could be found at http://discovery.informatics.uab.edu/PGC/ or https://figshare.com/projects/Polar_Gini_Curve/76749.

Distribution And Spatial Pattern Analysis On Malnutrition Cases: A Case Study In Pontianak City

@#Based on the Basic Health Research (Riskesdas) in 2018, malnutrition cases in West Kalimantan reached 23.8 percent. In 2015, Pontianak City documented 27 cases of malnutrition. Then, the cases increased in 2016 and 2017 as many as 29 and 41 cases. The utilization of Geographic Information System (GIS) is required as a method for public health surveillance and monitoring. This study aims to analyze the distribution of malnutrition cases based on several clinical and non-clinical factors using GIS between 2016 to 2017. The dependent variable was malnutrition cases and the independent variables included household income level, parent’s educational level, comorbidities factors, and distance to the primary health care service. A total of 65 cases of malnutrition in Pontianak City were collected from six sub-districts in Pontianak City. This research was a cross-sectional study. The results showed that of 65 cases of malnutrition occurred on under 5-year-old children in Pontianak in 2016-2017, malnutrition cases taking place in East Pontianak sub-district were 29 cases (44.6%). In addition, malnutrition with clinical symptoms was reported 63 cases (96.9%), while the distance from home to primary health care less than 1 km was 32 cases (49.23%). The study also revealed that malnutrition with comorbidities were 78,5%. Finally, household income levels with malnutrition were below Pontianak regional minimum wage (Rp 2,515,000/month or $176,88). The mapping of malnutrition cases using Geographic Information Systems can facilitate the nutrition programmer in Pontianak City Health Office and Public Health Centre in intervening the social determinant of health to overcome malnutrition.

Spatial pattern of poverty alleviation in traditional Chinese medicinal materials industry and its main influencing factors / 中草药

Based on the data of “National Chinese Medicine Resources Census and Germplasm Sharing Data Special Service-Poverty Alleviation of Chinese Medicine Industry” and “Kangmei Chinese Medicine Network-Service Platform of Chinese Medicine Whole Industry Chain”, the information of traditional Chinese medicinal materials (TCMM) resources in poverty-stricken areas was collated and analyzed, the database of planting area and output value of Chinese medicine in poverty-stricken areas was constructed, and the species in poverty-stricken areas were plotted by ArcGIS software. The spatial distribution map of the situation of herbal medicine planting can discover and summarize the spatial pattern characteristics and development rules of poverty alleviation in Chinese herbal medicine industry. On this basis, by referring to the relevant reports of “China Poverty Reduction Database” and “Office of the Leading Group for Poverty Alleviation and Development of the State Council”, this paper comprehensively analyses the main factors affecting poverty alleviation in the traditional Chinese medicine industry, and puts forward corresponding suggestions, hoping to provide beneficial references for the extensive poverty alleviation work in poor areas.

Recognition method of single trial motor imagery electroencephalogram signal based on sparse common spatial pattern and Fisher discriminant analysis / 生物医学工程学杂志

This paper aims to realize the decoding of single trial motor imagery electroencephalogram (EEG) signal by extracting and classifying the optimized features of EEG signal. In the classification and recognition of multi-channel EEG signals, there is often a lack of effective feature selection strategies in the selection of the data of each channel and the dimension of spatial filters. In view of this problem, a method combining sparse idea and greedy search (GS) was proposed to improve the feature extraction of common spatial pattern (CSP). The improved common spatial pattern could effectively overcome the problem of repeated selection of feature patterns in the feature vector space extracted by the traditional method, and make the extracted features have more obvious characteristic differences. Then the extracted features were classified by Fisher linear discriminant analysis (FLDA). The experimental results showed that the classification accuracy obtained by proposed method was 19% higher on average than that of traditional common spatial pattern. And high classification accuracy could be obtained by selecting feature set with small size. The research results obtained in the feature extraction of EEG signals lay the foundation for the realization of motor imagery EEG decoding.

Incidencia de iccendios sobre la vegetación de unDinamarca y bogotá d.c. (Coloombia), entre 2001 y 2110 / Fire Incidence on Vegetation in Cundinamarca and Bogota D.C. (Colombia) During the 2001-2010 Period

En este trabajo se analizó la distribución temporal y espacial de incendios respecto a las coberturas vegetales del departamento de Cundinamarca y Bogotá D.C., en el periodo 2001-2010. A partir de datos de focos activos provenientes de MODIS, se encontró que los incendios en el área de estudio siguen un patrón constituido por eventos en las dos temporadas secas (enero-marzo y julio-septiembre), destacando además que la incidencia es causada por poca precipitación e intervención del hombre en espacios naturales. Las poblaciones más afectadas son Caparrapí: 159 incendios, Bogotá: 152 incendios y Guaduas: 101 incendios. Bogotá registra la mayoría de sus incendios en la parte sur, localidad de Sumapaz. En cuanto a áreas protegidas del departamento el parque con más registros de focos de incendios es el Parque Nacional Natural Sumapaz (84), seguido por el Distrito de Manejo Integrado Cuchilla de San Antonio (21) y la Reserva Forestal Protectora Páramo Grande (9). Entre la vegetación afectada se destacan pastos, arbustos, matorrales y sus mosaicos, resaltando altos valores de incidencia sobre la vegetación de páramo y subpáramo. Las partes centro y noroccidentales, sur y surorientales del departamento, son las que presentan más conflagraciones, la mayoría se ubican entre los 0 a 1.000 msnm y 3.000 a 4.000 msnm. Finalmente los incendios en el área de estudio muestran un patrón asociado al clima y en particular a la temporada seca, pero también un patrón altitudinal. Las áreas de PNN, de protección y conservación regionales, son efectivas contra los incendios.

This work aims to use remote sensing as a method for determining fire dynamics in the department of Cundinamarca and the city of Bogotá D.C. in Colombia, by analyzing the temporal and spatial distribution of fires and the different types of vegetation affected in the 2011-2010 period. Based on MODIS fire hotspots, we found that the pattern fires in the study area are within the national standard, which includes increased number of events during the dry seasons (January-March and July September). The fire incidence is caused by low rainfall that complements the root causes of ignition, which are mainly started by human intervention. The most affected populations are Caparrapí with 159 fires; Bogotá with 152 fires and Guaduas with 101 fires. Bogotá recorded most of their fires within protected areas in the south, in the area of Sumapaz. Sumapaz National Park (84), followed by the District Integrated Management Cuchilla de San Antonio (21) and Protective Forest Reserve Páramo Grande (9). Among the vegetation affected we can find grasses, shrubs, bushes and mosaics, emphasizing high values of impact on vegetation of páramo and subpáramo. The central and northwestern parts, south and southeast parts of the department, are those with more outbreaks, and most of them are between 0 to 1,000 masl and 3,000 to 4,000 masl. Finally active fires in the study area follow a pattern associated to the climate and in particular to the dry season but also show an altitudinal pattern. National and regional protected areas are effective against fires.

Slope variation and population structure of tree species from different ecological groups in South Brazil

Size structure and spatial arrangement of 13 abundant tree species were determined in a riparian forest fragment inParaná State, South Brazil (23"16'S and 51"01'W). The studied species were Aspidosperma polyneuron Müll. Arg., Astronium graveolens Jacq. and Gallesia integrifolia (Spreng) Harms (emergent species); Alseis floribunda Schott, Ruprechtia laxiflora Meisn. and Bougainvillea spectabilis Willd. (shade-intolerant canopy species); Machaerium paraguariense Hassl, Myroxylum peruiferum L. and Chrysophyllum gonocarpum (Mart. & Eichler ex Miq.) Engl. (shade-tolerant canopy species); Sorocea bonplandii (Baill.) Bürger, Trichilia casaretti C. Dc, Trichilia catigua A. Juss. and Actinostemon concolor (Spreng.) Müll. Arg. (understory small trees species). Height and diameter structures and basal area of species were analyzed. Spatial patterns and slope correlation were analyzed by Moran's / spatial autocorrelation coefficient and partial Mantel test, respectively. The emergent and small understory species showed the highest and the lowest variations in height, diameter and basal area. Size distribution differed among emergent species and also among canopy shade-intolerant species. The spatial pattern ranged among species in all groups, except in understory small tree species. The slope was correlated with spatial pattern for A. polyneuron, A. graveolens, A. floribunda, R. laxiflora, M. peruiferum and T. casaretti. The results indicated that most species occurredin specific places, suggesting that niche differentiation can be an important factor in structuring the tree community.

Visando contribuir para o conhecimento das estratégias devida de espécies em fragmentos florestais, foram determinadas as estruturas de tamanho e espacial de 13 espécies arbóreas do remanescente de floresta ciliar no Estado do Paraná, no Sul do Brasil (23"16'S e 51"01'W). Foram analisadas as espécies: Aspidosperma polyneuron Müll. Arg., Astronium graveolens Jacq. e Gallesia integrifolia (Spreng) Harms, (emergentes); Alseis floribunda Schott, Ruprechtia laxiflora Meisn. e Bougainvillea spectabilis Willd. (dossel, intolerantes à sombra); Machaerium paraguariense Hassl, Myroxylum peruiferum L. e Chrysophyllum gonocarpum (Mart. & Eichler exMiq.) Engl. (dossel, tolerantes à sombra); Sorocea bonplandii (Baill.) Bürger, Trichilia casaretti C. Dc, Trichilia catigua A. Juss. e Actinostemon concolor (Spreng.) Müll. Arg. (subosque). Analisou-se a estrutura de diâmetro de cada espécie. Para a análise do padrão espacial e correlação com adeclividade foram utilizados o Índice de Autocorrelação espacial de Moran e o Teste Parcial de Mantel, respectivamente. Os grupos das árvores emergentes e das espécies de subosque apresentaram as maiores e as menores variações na altura e no diâmetro e maior e menor área basal, respectivamente. Diferenças nas estruturas de diâmetro foram observadas entre as espécies emergentes e entre as espécies de dossel intolerantes à sombra. O padrão espacial variou entre as espécies de todos os grupos, exceto as espécies de subosque tolerantes à sombra. A topografia estava relacionada com a distribuição espacial de A. polyneuron, A. graveolens, A. floribunda, R. laxiflora, M. peruiferum e T. casaretti. A análise dos resultados indicou que para cada espécie a maioria dos indivíduos ocorriam em locais específicos, sugerindo que a diferenciação de nicho pode estar relacionada à estruturação desta comunidade arbórea.

Distribución espacio-temporal de variables fisicoquímicas y biológicas en el hábitat del tiburón ballena Rhincodon typus (Orectolobiformes: Rhincodontidae) al norte del Caribe Mexicano

Spatial and temporal distribution of physicochemical features in the habitat of whale shark Rhincodon typus (Orectolobiformes: Rhincodontidae) in the north of Mexican Caribbean. Large groups of whale sharks (Rhincodon typus) are common in the North Mexican Caribbean and gather between May and September each year. We describe their spatial and temporal distribution, and the physicochemical (temperature, dissolved oxygen, light extinction coefficient and salinity) and biological conditions during the presence and absence seasons of R. typus. A total of 26 sampling stations were monitored to record whale shark sightings and physicochemical variables during 10 field campaigns from April 2005 to March 2006. At each station, zooplankton and water samples, for chlorophyll-a and nutrients determination, were collected. Physicochemical conditions were significantly different between presence-absence seasons (ANOSIM, Rglobal = 0.632). The R. typus season was characterized by low salinity values, and higher temperature, chlorophyll-a, dissolved oxygen and inorganic nitrogen concentrations values. Average zooplankton biomass was lower during the absence season, while recorded the maximum values during the presence one. Furthermore, these values were also observed in areas with higher species abundances, supporting the hypothesis that the site is used by R. typus primarily as a foraging area. We conclude that physicochemical conditions of the study area promote the biological productivity, which explains the spatial and temporal variability of R. typus. Rev. Biol. Trop. 58 (1): 399-412. Epub 2010 March 01.

En la zona marina ubicada al norte del Caribe Mexicano se congregan grandes grupos de tiburón ballena (Rhincodon typus) entre mayo y septiembre de cada año. Se describe la variación espacio-temporal de la distribución del tiburón ballena al norte del Caribe mexicano y las condiciones fisicoquímicas y biológicas que prevalecen en la zona durante la temporada de presencia y ausencia de R. typus. De abril de 2005 a marzo de 2006, 26 estaciones de muestreo fueron monitoreadas registrando avistamientos de tiburón ballena y variables fisicoquímicas (temperatura, oxígeno disuelto, coeficiente de extinción de luz y salinidad) en 10 salidas de campo. En cada estación fueron recolectadas muestras zooplancton y de agua para determinación de clorofila-a y nutrientes. Las condiciones fisicoquímicas fueron significativamente diferentes entre temporadas (ANOSIM, Rglobal=0.632). La temporada de presencia de R. typus estuvo caracterizada por valores bajos de salinidad, mayores valores de temperatura y oxígeno disuelto; mayores de nitrógeno inorgánico disuelto y concentraciones de clorofila-a y aunque la biomasa promedio de zooplancton fue menor que en la temporada de ausencia de R. typus, los valores máximos de biomasa zooplanctónica se registraron en el periodo de presencia y en sitios donde se registraron las mayores abundancias de la especie, apoyando la hipótesis de que el sitio es utilizado por la especie principalmente como zona de alimentación. Las condiciones fisicoquímicas de la zona de estudio que favorecen la productividad biológica explican la variabilidad espacial y temporal de R. typus al norte del Caribe Mexicano.