bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking Variant Identification Tools for Plant Diversity Discovery
Authors: Wu Xing , Heffelfinger Christopher , Zhao Hongyu , Dellaporta Stephen L. 
Published: May 2019

Abstract
Background

The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing data were originally developed and tested in human studies, raising questions as to their efficacy for plant research. A detailed evaluation of the entire variant calling pipeline, including alignment, variant calling, variant filtering, and imputation was performed on different programs using both simulated and real plant genomic datasets.

Results

A comparison of SOAP2, Bowtie2, and BWA-MEM found that BWA-MEM was consistently able to align the most reads with high accuracy, whereas Bowtie2 had the highest overall accuracy. Comparative results of GATK HaplotypCaller versus SAMtools mpileup indicated that the choice of variant caller affected precision and recall differentially depending on the levels of diversity, sequence coverage and genome complexity. A cross-reference experiment of S. lycopersicum and S. pennellii reference genomes revealed the inadequacy of single reference genome for variant discovery that includes distantly-related plant individuals. Machine-learning-based variant filtering strategy outperformed the traditional hard-cutoff strategy resulting in higher number of true positive variants and fewer false positive variants. The 2-step imputation which utilized a set of high-confidence SNPs as the reference panel showed up to 60% higher accuracy than direct LD-based imputation method.

Conclusions

Programs in the variant discovery pipeline have different performance on plant genomic dataset. Choice of the programs is subjected to the goal of the study and available resources. This study serves as an important guiding information for plant biologists utilizing next-generation sequencing data for diversity characterization and crop improvement.
miR-147b-modulated expression of vestigial regulates wing-morph differentiation in the bird cherry-oat aphid Rhopalosiphum padi
Authors: Fan YJ , Li XX , Mohammed Abd Allah A. H. , Liu Y , Gao Xiwu 
Published: May 2019

Abstract
Background

The wing polyphenism occurs under crowding and nutrition-deficiency conditions in most aphid species. Although the influence of environmental factors on wing polyphenism of aphids have been extensively investigated, molecular mechanisms underlining wing-morph differentiation has not been fully understood.

Results

The expression levels of the twenty genes involved in wing patterning network were examined, and only vestigial (vg) showed significantly different expression levels in both whole-body and wall-body of third nymphal instars, with 5.4- and 16.14- fold higher in winged lines compared to wingless lines, respectively in Rhopalosiphum padi. Moreover, vg expressions were higher in winged aphids compared to that in wingless aphids of third, fourth instar nymphs and adults, and larger difference ratio were observed in third (21.38-fold) and fourth (20.91-fold) instar nymphs relative to adult (3.12-fold) between wing morphs. Suppression of vg using RNAi repressed the wing development of third winged morphs. Furthermore, modulation of miR-147b levels by microinjection of its mimics decreased vg expression levels and repressed wing development.

Conclusions

Our findings suggest that vg is essential for wing development and that miR-147b modulates its expression. To our knowledge, our results provide an empirical evidence that miRNA is involved in the regulation of wing morphs in aphids.
Genome-wide analysis and expression profiles of the StR2R3-MYB transcription factor superfamily in Solanum Tuberosum
Authors: Li Yuanming , Lin-Wang Kui , Liu Zhen , Allan Andrew C. , Zhang Junlian , Liu Yuhui 
Published: May 2019

Abstract
Background: MYB transcription factors comprise one of the largest families in plant kingdom, which play a variety of functions in plant developmental processes and defence responses. However, it has not been systematically studied in Potato (Solanum tuberosum), which is the most important non-cereal crop world-wide.
Results: In the present study, a total of 108 StR2R3-MYB transcription factors were identified and further phylogenetically classified into 28 subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that the segmental duplication events played a crucial role in the expansion of StR2R3-MYB gene family. Synteny analysis indicated that 37 and 13 StR2R3-MYB genes were orthologous to Arabidopsis and wheat, respectively, and these gene pairs have evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-preferential and abiotic stress-responsive StR2R3-MYB genes. We further analyzed StR2R3-MYB genes might be involved in anthocyanin biosynthesis and drought stress by using RNA-seq data of pigmented tetraploid potato cultivars and drought-sensitive and -tolerant tetraploid potato cultivars under drought stress, respectively. Moreover, EAR motifs were found in 21 StR2R3-MYB proteins and 446 pairs of proteins were predicted to interact with 21 EAR motif-containing StR2R3-MYB proteins by constructing the interaction network with medium confidence (0.4). Additionally, Gene Ontology (GO) analysis of the 21 EAR motif-containing StR2R3-MYB proteins was performed to further investigate their functions.
Conclusions: In this work, we systematically identified StR2R3-MYB genes by analyzing the potato genome sequence using a set of bioinformatics approaches. Genome-wide comparative analysis of StR2R3-MYB genes and their expression analysis identified members of this superfamily may be involved in tissue-specific development, anthocyanin biosynthesis and abiotic stress responses.
“Moro lá no Cordu”-Conhecendo a comunidade a partir do olhar das crianças
Authors: Magalhães Silvana Bezerra de Castro 
Published: May 2019

O presente trabalho situa-se no universo de crianças do projeto social CASA- situado no Cordoeira, comunidade vulnerável de Nova Friburgo-RJ. O projeto iniciou suas ações no contra-turno escolar no ano de 2017 e vem construindo suas ações sociopedagógicas numa perspectiva das crianças como protagonistas do processo.Uma das necessidades e objetivos desse trabalho foi conhecer o contexto da comunidade, a partir do olhar das próprias crianças, para o estudo das realidades de infância Para isso, uma das ações que analisamos foi a pesquisa realizada com as crianças sobre o contexto vivido, sobre sua comunidade e recortes das próprias sobre esse lugar físico e simbólico, tendo como grande desafio teórico-metodológico considerar as crianças atores sociais plenos, valorizando seus processos de apropriação, reinvenção e reprodução .A metodologia utilizada partiu das concepções das crianças através da realização de oficinas que favorecessem a escuta das imagens e vivências sobre sua comunidade (diferentes linguagens artísticas). Crianças têm o direito de dizer a sua palavra a partir do seu “saber de experiência feito”. (FREIRE, 1997, 1998)O processo, ainda em construção, já indicou olhares enriquecedores de como as crianças se adaptam as dificuldades do contexto, bem como criam soluções novas para lidar com problemas e a ludicidade presente no cotidiano da comunidade.
ANALISIS KESESUAIAN LAHAN UNTUK TANAMAN JERUK DI KELURAHAN PEGAGAN JULU I KECAMATAN SUMBUL KABUPATEN DAIRI
Authors: Sipayung Edi Valdo , Astuti Anik Juli Dwi 
Published: May 2019

Tujuan penelitian ini untuk mengetahui: 1) Karakteristik lahan yang dilihat dari suhu, ketersediaan air, kondisi perakaran, daya menahan hara, ketersediaan unsur hara dan topografi untuk lahan jeruk di Kelurahan Pegagan Julu I Kecamatan Sumbul Kabupaten Dairi. 2) Kesesuaian lahan untuk tanaman jeruk dilihat dari karakteristik lahan (suhu, ketersediaan air, kondisi perakaran, daya menahan hara, ketersediaan unsur hara dan topografi) di Kelurahan Pegagan Julu I Kecamatan Sumbul Kabupaten Dairi. Penelitian ini dilakukan di Kelurahan Pegagan Julu I Kecamatan Sumbul Kabupaten Dairi tahun 2017. Populasi dalam penelitian ini ialah seluruh lahan kering di Kelurahan Pegagan Julu I seluas 146 Ha. Sampel ditentukan secara Stratified Random Sampling berdasarkan kelas kemiringan lereng daerah penelitian. Teknik pengumpulan data yang dilakukan ialah observasi, pengukuran dan studi dokumenter. Teknik analisis yang digunakan adalah teknik analisis deskriptif kualitatif. Hasil penelitian menunjukkan bahwa: 1) Karakteristik lahan di Kelurahan Pegagan Julu I cukup baik untuk peruntukan tanaman jeruk. Hal ini didukung oleh rata-rata suhu harian sebesar 21,50C dan curah hujan tahunan sebesar 1.794 mm/tahun yang baik untuk tanaman jeruk. Beberapa karakteristik lahan yang lain juga mendukung tumbuhnya tanaman jeruk karena memiliki drainase yang agak baik, tekstur lempung berpasir, kedalaman tanah yang dalam sekitar 78-94 cm, KTK liat yang cukup sebesar 8,37-11,34, pH H2O yang normal antara 5,67-6,12, P2O5 sebesar 10,24-13,09 ppm dan tidak terdapatnya batuan di permukaan serta singkapan batuan. Karakteristik yang menghambat tumbuhnya tanaman jeruk ialah ketersediaan N-Total yang rendah dan kemiringan lereng yang terjal dengan persentase luas lahan sebesar 2% dari keseluruhan lahan di kelurahan tersebut. 2) Kelurahan Pegagan Julu I berada pada kelas kesesuaian lahan S2sr. Lahan yang memiliki pembatas paling banyak adalah satuan lahan IV dan V dengan persentase luas lahan sebesar 5% dari keseluruhan lahan dan faktor pembatasnya ialah ketersediaan N-Total yang berada pada kelas S3 dan Kemiringan lereng yang berada pada kelas N. Sedangkan lahan yang memiliki pembatas paling sedikit adalah satuan lahan I, II dan III dengan persentase luas sebesar 95% dari keseluruhan lahan. Faktor pembatas ringan pada satuan lahan ini yaitu KTK, N-Total, P2O5 dan kemiringan lereng yang masing berada pada kelas S2. Drainase, tekstur, pH, batuan permukaan dan singkapan batuan menjadi faktor pendukung di satuan lahan ini karena masing-masing berada pada kelas S1. Kata kunci: kesesuaian lahan, suhu, ketersediaan air, kondisi perakaran, daya menahan hara
ANALISIS PERUBAHAN GARIS PANTAI MENGGUNAKAN DATA PENGINDERAAN JAUH DI PANTAI CERMIN, KABUPATEN SERDANG BEDAGAI
Authors: Lozi Andrian , Rahmad Riki 
Published: May 2019

Artikel ini ditulis untuk mengetahui yaitu penggunaan data penginderaan jauh yang dihasilkan oleh teknologi penginderaan jauh untuk menganalisis perubahan garis pantai di Pantai Cermin Kabupaten Serdang Bedagai. Metode yang dilakukan dalam penelitian ini adalah deskriptif kuantitatif yaitu menentukan sebaran, luasan dan perubahan tutupan lahan yang diperoleh dengan menganalis Citra Landsat 4-5 pada tahun 2007 dan Citra Landsat 2017 tentang perubahan garis pantai berdasarkan citra 2007 dan ditumpangsusun (superimposition) dengan citra klasifikasi tahun 2017. Berdasarkan hasil dari interpretasi yang di lakukan dengan menggunakan software ArcGIS 10.5 maka di dapatkan luas wilayah di Kecamatan Pantai Cermin yang bertambah pada tahun 2007 dan 2017 mencapai 1481798 km². Penambahan wilayah tersebut tersebar di sepanjang pesisir kawasan Kecamatan Pantai Cermin, serta dengan rata – rata pengikisan oleh abrasi air laut sebesar 1249322 Km² per tahunnya, dengan penambahan tepi pantai yang cukup signifikan per tahunnya.Kata Kunci: Perubahan Garis Pantai, Abrasi, Sedimentasi, Landsat
Wind-induced stem breakage height effect on potentially recovered timber value: case study of the Scots pine (Pinus sylvestris L.) in Latvia
Authors: Dubrovskis Edgars , Donis Janis , Racenis Eduards , Kitenberga Mara , Jansons Aris 
Published: May 2019

Abstract
In Europe, salvage-logging is a common management activity to partially recover economic value from wind disturbed forests. In the near future, wind damage to forests is predicted to increase due to climate change. Therefore, an economic assessment of wind damage effects on recovered timber value is useful information in the decision-making process. In this study, we aim to assess the influence of different stem damage heights on the monetary value of recovered timber. We simulated stem breakage at three heights for the Scots pine (Pinus sylvestris L.): 3, 5, and 7 m. For comparison, we used an uprooted tree without stem breakage. Our results revealed that the most negative influence on the recovered timber value was stem breakage at 3 m, which decreased the monetary value by 35%. The stem breakage at 5 and 7 m decreased the recovered timber value by 9–10%. Over the analysed period (2006–2017), no significant differences in the monetary value of the recovered timber were found between uprooted lumber and stems with breakage at 5 and 7 m. The price fluctuations in the market have a significant influence on the recovered timber value, which might cause a larger decrease in monetary value than stem breakage.
Ground vegetation composition and diversity in drained Norway spruce (Picea abies (L.) Karst.) stands 50 years after whole-tree harvesting management: case study in Latvia
Authors: Čakšs Roberts , Robalte Linda , Desaine Iveta , Džeriņa Baiba , Jansons Aris 
Published: May 2019

Abstract
The long-term (50 years) effect of whole-tree harvesting (stump harvesting) on ground vegetation in experimental drained Norway spruce (Picea abies (L.) Karst.) stands was studied. We used a chronosequence approach to assess the long-term impact of whole-tree harvesting (WTH) on stands’ ground vegetation. WTH stands were compared with four control stands with different age and with the same forest type: young stand (15 years), middle-aged stand (45 years), mature stand (110 years) and over-mature stand (140 years). Species richness was similar between the WTH stand and middle-aged stand (61 and 60 species, respectively). Shannon-Wiener diversity indices in the WTH and middle-aged stand (3.40 and 3.19, respectively) indicated that the stands were similar to each other. A community similarity analysis showed that the composition of vegetation was similar between the WTH and middle-aged stand, although some species like Lycopodium clavatum and Diphasiastrum complanatum occurred only in the WTH stand. The study showed that a period of 50 years is sufficient for ground vegetation of a typical drained spruce forest to recover after WTH management.
Assessment of Western taiga habitat in Lahemaa National Park, Estonia
Authors: Paluots Teele , Franklin Jerry F. , Maamets Lembit , Laarmann Diana , Kangur Ahto , Korjus Henn 
Published: May 2019

Abstract
Diverse structural elements play an important role in sustaining biodiversity in old-growth forests. Therefore, it is important to have thorough knowledge about these habitats and their condition in protected areas. Metsakorralduse Büroo OÜ conducted a large-scale Natura 2000 forest habitat inventory that covered 60% of Lahemaa National Park (LNP) area. Western taiga habitat data (7,191 ha) from this inventory was used for analysis of forest stages. The data was grouped according to stand classes by total area and these classes were compared by deadwood occurrence and relative density. For more precise evaluation of coarse woody debris (CWD) we used 27 sample plots from the Estonian Network of Forest Research Plots (ENFRP) located in LNP. The biggest areas of Western taiga habitat were covered by mature and old stages. CWD occurrence (over 5 m3ha−1 of snags and logs) by habitat representativeness is higher in old and natural forest classes. This logical result is overshadowed by the outcome that the CWD was not substantially present on 32% of the area in the old-growth forest class. This indicates that these areas lack the potential of biological legacies to provide critical niche habitats for different species. The study shows that the CWD quantity in Estonian conditions is similar to that reported in previous studies in this region, but because many of the older forest stage classes do not have any CWD present, these areas should include ecological restoration practices in their conservation planning. By creating snags, logs and gaps in these areas, we are able to create better structural variability and include wood into different decay processes.
The effect of planting stock and soil scarification on forest regeneration
Authors: Jäärats Andres , Tullus Arvo 
Published: May 2019

Abstract
The present research is a comparative analysis of how the main quality indices of containerized and barerooted coniferous (Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris L.)) planting stock conform to the existing standards in Estonia, how the plantation development depends on planting stock and natural regeneration on soil scarification. The height of Scots pine containerized seedlings exceeded that of barerooted seedlings by 20%. The height of barerooted Norway spruce transplants exceeded that of containerized seedlings by 19%. The root-collar diameter of containerized pine stock formed 70% and the corresponding index of containerized spruce stock formed 48% of the diameter of the barerooted plants of the same species. Typically, containerized plants had better initial growth increment during the first two to three years after planting but this difference disappeared during the latter years. The growth of Scots pine barerooted and containerized seedlings was similar, while the growth of Norway spruce containerized seedlings was slightly inferior compared to barerooted plants. Survival of both test species was independent of planting stock used. After clear-cutting, certain areas of peatland and mineral areas were disc-trenched and inventoried at the end of the first growing season. The number of all woody plants was determined by microsites – untreated area, furrow, slope, and ridge. The same inventory was repeated 11 growing seasons later. After 11 growth years, a large number of Scots pine trees was found in Rhodococcum, Oxalis and Vaccinium myrtillus site types and drained peatlands. The number of pine plants on microsites on mineral soil was the greatest in furrows and on slopes (34% and 30%), and on peat soil on furrows and in untreated areas (47% and 53%). The number of naturally regenerated Norway spruce trees was the largest in Vaccinium myrtillus, Oxalis-Rhodococcum and Oxalis site types. With regard to microsites, spruce plants were the most abundant in furrows and ridges on mineral soil (31% and 24%) and in untreated areas and on slopes on peat soil (46% and 42%).
Sociedade e Multiculturalismo: Uma reflexão a luz da Lei de Diretrizes e Bases da Educação Nacional (LDB)
Authors: Silva Graciete Barros , Souza Janaene Leandro de 
Published: May 2019

Objetivos: Compreender como as instituições escolares trabalham com a educação multicultural na atual conjuntura social e política, destacando os conflitos situados na nossa sociedade que estão relacionados ao conhecimento da multicultura. Métodos: Trata-se de um estudo de abordagem qualitativa, como técnica de coleta de dados usou-se a pesquisa bibliográfica. Resultados: Vivemos em um mundo que ainda predomina o pensamento homogêneo (cultura única), intolerante a diversidades e a existência de diferentes grupos étnicos. Considerações finais: Torna-se necessário uma análise desses sistemas educativos para que se possa alcançar o que está previsto na Lei de Diretrizes e Bases da Educação Nacional 9394/96, que define regularizar o sistema de educação com base na constituição com o objetivo de tornar a educação para todos, construindo assim uma relação recíproca entre os indivíduos, relações estas que produziram mudanças e reforçará a identidade de cada individuo.
Perfil epidemiológico da dengue em um estado do nordeste brasileiro, 2011 a 2015
Authors: Santos Leila Karoline Ferreira dos , Pessôa Valleska Maria Leão , Santos Tâmyssa Simões dos , Bragagnollo Gabriela Rodrigues , Machado Gabriel Pinheiro , Munõz Susana I. Segura , Bragagnollo Stephanie Rodrigues , Guimarães Marcela das Neves , Carvalho Lucyo Wagner Torres de 
Published: May 2019

Objetivo: Analisar o perfil epidemiológico da dengue em um estado do nordeste brasileiro no período de 2011 a 2015. Método: Trata-se de um estudo epidemiológico descritivo de abordagem quantitativa. Resultados: No período de 2011 a 2015, foram notificados 111.773 casos de Dengue no estado de Alagoas, o que resulta em 686,4 casos por 100.000 habitantes. Neste período, os maiores coeficientes de detecções deram-se nos anos de 2012 e 2015, em todas as mesorregiões de Alagoas, com aumento do coeficiente de detecção média do período. Evidenciou-se maior ocorrência dos casos no sexo feminino, de cor parda, em moradores da zona urbana, de faixa etária adulta e com escolaridade até o ensino fundamental. Conclusão: A dengue continua como importante agravo, tendo em vista sua alta incidência, com períodos epidêmicos, e possibilidade de evolução para o óbito. Possuindo assim, grande repercussão para saúde pública do Estado e do país.
Enfermagem perioperatória e sua inserção nos planos de ensino das universidades
Authors: Almeida Mailma Costa de , Silva Nair Chase da , Sabino Aderlaine da Silva 
Published: May 2019

Objetivo: Investigar a inserção da Enfermagem Perioperatória nos Planos de Ensino das Universidades de Manaus/AM. Método: descritivo-exploratório, qualitativo, baseado na análise categorial temática, em duas universidades públicas de Manaus/AM, com seis docentes que ministram conteúdos de Enfermagem Perioperatória. A produção foi obtida por meio de entrevista e grupo focal. Resultados: Os docentes eram do sexo feminino, com experiência na docência e assistência de Enfermagem Perioperatória; os planos de ensino permitem uma visão parcial da Enfermagem Perioperatória; de quatro disciplinas três possuem carga horária teórico-prática e apenas uma prática; nas ementas e conteúdos estão em duas disciplinas de maneira explicita e duas implícita; os objetivos constam em três disciplinas; o conteúdo estão direcionados a Enfermagem Perioperatória; as estratégias de ensino os docentes sentem a necessidade de trabalhar com metodologias inovadoras; os recursos de ensino são compatíveis com as estratégias de ensino; as referências bibliográficas situam-se entre 2005 a 2015 e período anterior a 2004, não se constatou a existência de periódicos, artigos científicos, teses e dissertações, sites e outros. Conclusão: O ensino da EP nas IES públicas esteve presente na formação do enfermeiro, entretanto, precisa de ações que qualifiquem na perspectiva de atender às DCN e saúde da população.