bluuebunny/crossref_metadata_2025 huggingface dataset:
MORFOMETRIA DE BACIAS HIDROGRÁFICAS DE PRIMEIRA ORDEM EM ÁREAS AGRÍCOLAS SOB SISTEMA PLANTIO DIRETO: DELIMITAÇÃO E PROPENSÃO À EROSÃO E INUNDAÇÃO
Authors: Sabino Hullysses , Vasques Gustavo M. , Hermani Luis Carlos , Dart Ricardo O.
Published: July 2020

O Sistema Plantio Direto (SPD) aplica técnicas agrícolas conservacionistas para preservação do solo, controlando processos de erosão. Para isso, é necessário conhecer as características do relevo que afetam a dinâmica e o poder erosivo da água na microbacia hidrográfica (MBH) em que o SPD está inserido. Os objetivos do trabalho foram: adaptar uma metodologia para o delineamento de 12 MBHs de cerca de 1 km² sob SPD a partir de modelos digitais de terreno (MDTs) e de elevação (MDEs). Ademais, calcularam-se quatro índices morfométricos relacionados à dinâmica e poder erosivo da água nas MBHs: declividade, coeficiente de compacidade (CC), índice de circularidade (IC) e fator de forma (FF). Para delimitar as MBHs foi necessário combinar dados de diferentes fontes e resoluções espaciais (MDTs Pleiades e Ultracam D, MDEs ALOS Palsar e SRTM) e usou-se a extensão ArcSWAT. As MBH estavam distribuídas nos seguintes estados: SP, GO, MS, RS e PR. Conforme os valores de declividade, as MBHs Sarandi e Coxilha são as mais propensas à erosão, enquanto Maracaju 1 e Itaí 1 são as menos propensas. Segundo os índices CC, IC e FF, as MBHs Toledo 2 e Coxilha são as mais propensas à inundação, e as MBHs Maracaju 1 e 2 e Itaí 1 as menos. A metodologia aplicada foi adaptada com êxito para a delimitação de MBHs de primeira ordem. Outrossim, os índices morfométricos calculados subsidiarão a gestão do SPD, permitindo executar medidas de controle da erosão, reduzindo impactos da perda de solo e nutrientes nessas áreas agrícolas.
INTENSIDADE DA ATIVIDADE TECTÔNICA E SUA ESPACIALIDADE NA BACIA DO RIO VERDE, SUL DE MINAS GERAIS: CONTRIBUIÇÕES PARA A REGIONALIZAÇÃO DA TECTÔNICA PÓS-MIOCÊNICA
Authors: Marques Neto Roberto
Published: July 2020

O controle morfotectônico na evolução do relevo vigente na região dos grandes escarpamentos do sudeste brasileiro tem sido expediente permanente de pesquisadores no campo das geociências, e o emprego de índices geomórficos tem sido uma das técnicas de pesquisa mais acionadas. O presente artigo visa discutir o controle tectônico vigente na bacia do Rio Verde (sul de Minas Gerais) associando diferentes índices geomórficos em um índice agregado (índice de intensidade atividade tectônica), aplicado nas sub-bacias de maior ordem. Os resultados não apenas corroboraram os esforços diastróficos neotectônicos regionais, mas também permitiram uma regionalização da atividade tectônica, diferenciando os contextos vigentes nas regiões geomorfológicas da Serra da Mantiqueira e do Planalto do Alto Rio Grande. A maioria das bacias mensuradas apresentou índice elevado, principalmente aquelas localizadas no contexto da Serra da Mantiqueira, coincidentes com as principais zonas de cisalhamento regionais.­­
PADRÕES DE EMPILHAMENTO ESTRATIGRÁFICO E SEUS REFLEXOS NA MORFOLOGIA DA BARREIRA COSTEIRA HOLOCÊNICA NO LITORAL MÉDIO DO RIO GRANDE DO SUL, BRASIL
Authors: Borges de Bitencourt Volney Junior , Dillenburg Sergio Rebello , Barboza Eduardo Guimarães , Rosa Maria Luiza Correa da Camara , Manzolli Rogerio Portantiolo
Published: July 2020

Neste trabalho, investigou-se com detalhe a barreira holocênica do litoral médio do Rio Grande do Sul (RS), entre as localidades do Estreito e de Bacupari. Este trecho do litoral corresponde a mais expressiva projeção costeira de larga-escala da costa do RS. Dados geofísicos (Georadar) e geomorfológicos superficiais permitiram importantes descobertas. Na porção sul da projeção costeira, entre o Estreito e o setor norte da Lagoa do Peixe, a barreira holocênica exibe um comportamento evolutivo dominantemente retrogradacional (provavelmente desde 6 ka até o presente), o qual foi determinado por um longo período de balanço negativo de sedimentos. Já na porção norte da projeção, entre o Balneário Mostardense e Bacupari, a barreira mostra uma inversão de comportamento retrogradacional para progradacional. Tal mudança evolutiva, expressa numa progradação que varia de 230 a 1800 m, é possivelmente oriunda de uma alteração no balanço de sedimentos (balanço negativo para positivo) que pode ter ocorrido somente há alguns séculos, ou mesmo poucos milênios. A mudança para um padrão de empilhamento progradacional mostrou-se crescente em dimensão (extensão do registro progradacional) do meio para o norte da projeção costeira. É possível sugerir que essas tendências evolutivas em escala geológica (10²-10³ anos) vão continuar no decorrer das próximas décadas. Informações acerca do comportamento evolutivo da linha de costa nos últimos séculos e milênios podem servir como subsídios do meio físico na gestão costeira do litoral médio do RS.
A colaboração compositor-intérprete para a composição e a interpretação de O Caldeirão dos esquecidos, de Danilo Guanais
Authors: De Moraes Holschuh Mariana , Bezerra de Queiroz Rucker , Noda Luciana
Published: July 2020

Este trabalho analisa e relata a colaboração compositor-intérprete para a escrita e para a construção da interpretação de O Caldeirão dos esquecidos, de Danilo Guanais (1965-). O método adotado envolveu o acompanhamento ativo da elaboração da composição e da interpretação, por parte dos pesquisadores-intérpretes, através de reuniões presenciais, trocas de correspondência eletrônica e telefonemas com o compositor. Os dados assim coletados foram cronologicamente registrados em diário eletrônico. Através da análise comparativa entre os esboços da obra e o conteúdo das reuniões, observou-se que a atuação dos pesquisadores-intérpretes impactou significativamente o resultado da composição, levando a alterações que afetaram, sobretudo, o idiomatismo da escrita da obra. Os dados coletados demonstram, ainda, que a colaboração influenciou a construção interpretativa para a estreia da peça por meio do contato direto com o compositor. Concluiu-se que a colaboração compositor-intérprete analisada impactou positivamente tanto a composição quanto a interpretação da obra.
O acervo Chiquinha Gonzaga em narrativas autobiográficas
Authors: Cantos Savelli Gomes Rodrigo
Published: July 2020

Nesta investigação analiso os documentos que constam no acervo da maestrina e compositora Chiquinha Gonzaga, hoje em posse do Instituto Moreira Salles do Rio de Janeiro. Trata-se de um material que começou a ser colecionado pelas mãos da própria artista, pelo qual foram conservados inúmeros fragmentos de sua própria vida, suas memórias, sua trajetória pessoal e profissional, de modo que, parte deste material, analiso como “representações de si”, ou seja, como possibilidade de narrativas autobiográficas. Com base nas noções de “cultura de si” e “formações discursivas”, de Foucault (2015), “biografemas”, de Barthes (1977), e “pacto autobiográfico”, de Lejeune (2014), recorro à Análise do Discurso, partindo do fundamento de que os conhecimentos que compõem o acervo constituem um sistema de enunciados, verdades parciais, intepretações históricas e culturalmente constituídas; portanto, mais do que descrevê-lo e interpretá-lo, interessa-me compreender os contextos – social e simbólico – de como o acervo foi constituído, modificado e produzido. A análise do material problematizou os mecanismos pelos quais os discursos e narrativas sobre a vida e obra de Chiquinha Gonzaga atravessaram o tempo, assim como as implicações do arquivamento da própria vida. Além disso, a análise revela o acervo como uma fonte privilegiada para compreensão do universo social feminino, uma alternativa diante da ausência de informações sobre artistas mulheres na historiografia musical brasileira, na qual, muitas vezes, a presença feminina é ignorada e desvalorizada.
Analisis Keterampilan Proses Sains Dan Self Regulation Biologi Kelas XI : Pengaruh Model Auditory, Intellectually dan Repatition (AUDI-IR)
Authors: Haka Nukhbatul Bidayati , Pratiwi Vanny Dhea , Anggoro Bambang Sri , Hamid Abdul
Published: July 2020

Hasil pembelajaran biologi yang belum tercapai secara baik dikarenakan rendahnya kemampuan berpikir siswa. Pembelajaran secara umum belum melibatkan laboratory skills, terjadinya passive learning, kurangnya interaksi antar siswa, pembelajaran jarang melibatkan learning society, penilaian masi bersifat sporadic yang jarang menilai secara utuh baik keterampilan proses, self regulation, maupun kemampuan berpikir siswa. Penelitian ini bertujuan untuk mengetahui pengaruh model pembelajaran Auditory, Intellectually, dan Repatition terhadap peningkatan Keterampilan Proses Sains dan Self Regulation pada peserta didik. Penelitian ini menggunakan metode quasi eksperimen dengan pretest dan posttest control group design, dengan teknik sampling Teknik acak kelas. Penelitian ini dilaksanakan di kelas XI di SMA Negeri 14 Bandar Lampung yang diterapkan dikelas kontrol (XI MIA2)  dan eksperimen (XI MIA3) pada materi sistem pencernaan tahun ajaran 2019/2020. Instrumen penelitian menggunakan tes dan lembar observasi keterampilan proses sains, angket Self Regulation. Analisis data menggunakan uji MANOVA. Berdasarkan hasil penelitian diketahui nilai ngain KPS kelas kontrol 0.45 (sedang) dan kelas eksperimen 0.67 (sedang), sedangkan nilai ngain self regulation kelas kontrol 0.36 (sedang), dan kelas eksperimen 0.52 (sedang). Sehingga dapat disimpulkan bahwa sig. 0,000 < 0,05 artinya terdapat pengaruh model pembelajaran Auditory, Intellectually, dan Repatition terhadap keterampilan proses sains dan self regulation pada kelas XI.
Discovery dan Pendekatan Jelajah Alam Sekitar (JAS) pada Pembelajaran Konsep Klasifikasi Makhluk Hidup
Authors: S Mansur , Xaverius Andre Pratama F
Published: July 2020

ABSTRAK

Penelitian ini bertujuan untuk mengetahui pengaruh pendekatan Jelajah Alam Sekitar (JAS) terhadap keaktifan dan hasil belajar peserta didik kelas VII SMP Muhammadiyah Waipare pada konsep klasifikasi makhluk hidup. Metode yang digunakan adalah quasi exsperimental design dengan desain nonequivalent control grub design. S Sampel pada penelitian ini adalah kelas VII C berjumlah 21 siswa sebagai kelas eksperimen dan kelas VII D berjumlah 20 siswa sebagai kelas kontrol. Teknik penentuan sampel menggunakan sampling purposive. Hasil analisis uji coba instrumen menunjukkan bahwa semua instrumen layak untuk di gunakan. Teknik analisis data meliputi uji normalitas, uji homogenitas dan uji hipotesis. Hasil uji normalitas menunjukkan bahwa sebaran  variabel hasil belajar tergolong normal dan hasil uji homogenitas menunjukkan bahwa varians data penelitian homogen. Hasil penelitian menunjukkan bahwa peserta didik sangat aktif mengikuti pembelajaran dengan menggunakan model pembelajaran Jelajah Alam Sekitar (JAS) pada konsep klasifikasi makhluk hidup. Hal ini ditunjukkan oleh hasil analisis keaktifan peserta didik sebesar  81,77. Selain itu, terdapat pengaruh yang signifikan antara model pembelajaran jelajah alam sekitar (JAS) terhadap hasil Belajar kelas VII SMP Muhammadiyah Waipare pada konsep klasifikasi makhluk hidup. Hal ini di tunjukkan oleh analisis uji t diperoleh nilai signifikansi < 0,05 yaitu (0,000 < 0,05).

 

Kata Kunci : Jelajah Alam Sekitar (JAS), keaktifan, hasil belajar
Identifikasi Biodiversitas Tumbuhan Pada Lingkungan Akuatik di Sungai Kabupaten Jepara
Authors: Afiyah Nor , Sa’adah Latifatus , Putri Handayani Putri , Laelasari Iseu
Published: July 2020

ABSTRAK
Penelitian ini bertujuan untuk mengidentifikasi biodiversitas tumbuhan pada lingkungan akuatik sungai di Kabupaten Jepara. Peneliti menggunakan metode deskriptif kualitatif dengan mengambil sampel empat plot stasiun penelitian secara purposive pada Sungai Batukali, Sungai Gerdu, Sungai Karang Aji dan Sungai Kedung Kabupaten Jepara. Pengumpulan data dilakukan dengan observasi, dokumentasi, identifikasi dan inventarisasi data kemudian dilakukan triangulasi sumber data untuk melakukan validasi dan analisis data lanjutan. Hasil penelitian mengungkap adanya biodiversitas tumbuhan air yang ditemukan disepanjang Daerah Aliran Sungai seperti Eichornia crassipes (eceng gondok), Nymphaea alba (teratai), Hydrilla verticillata (ganggeng), Ipomoea aquatic (kangkung), Nelumbo nucifera (seroja/lotus), Salvinia molesta (kiambang), Monochoria hastata (eceng), Echinodorus radicans (melati air), Sagittaria lancifolia (daun tombak). Dari tumbuhan akuatik yang ditemukan tersebut terdapat tumbuhan yang mendominasi pada stasiun tempat penelitian yaitu tumbuhan Eichornia crassipes dan Hydrilla verticillata.

 
Strategi Implementasi Kompetensi Guru Biologi dalam Pengembangan Pembelajaran Biologi di Era Disrupsi
Authors: Jannah Noor
Published: July 2020

Studi ini bertujuan untuk mengetahui strategi implementasi kompetensi guru biologi dalam pengembangan pembelajaran biologi di era disrupsi. Di era disrupsi ini terjadi perubahan yang sangat cepat dan sulit diprediksi di segala bidang termasuk pendidikan. Perubahan yang demikian, sekaligus dapat menjadi peluang dan tantangan bagi setiap individu. Guru sebagai subjek yang mengimplementasikan pendidikan harus memiliki kompetensi dalam menjalankan tugasnya. Menurut Undang-Undang Nomor 14 Tahun 2005 pasal 10 ayat 1 tentang Guru dan Dosen “Kompetensi guru meliputi kompetensi pedagogik, kompetensi kepribadian, kompetensi sosial, dan kompetensi profesional yang diperoleh melalui pendidikan profesi”. Studi ini dilakukan menggunakan metode studi pustaka yang diperoleh dari berbagai literatur seperti, jurnal dan buku, kemudian dianalisis dan diambil suatu kesimpulan. Seorang guru dalam melaksanakan pembelajaran harus dapat mengembangkan kreativitas dan inovasi dalam melaksanakan pembelajaran biologi di era disrupsi. Membuat perencanaan pembelajaran, pemilihan pendekatan, metode, dan teknik yang tepat dan relevan dengan perkembangan peserta didik, sehingga pembelajaran yang diperoleh akan berkesan. Kemampuan inilah terangkum dalam kompetensi guru.

 

Kata kunci: kompetensi guru biologi, pembelajaran biologi.
Traumatic Avulsion of Gluteus Tendons Associated With Posterior Fracture-dislocation of the Femoral Head
Authors: Busato Thiago Sampaio , Morozovski Marcelo Gavazzonni , Costantini Julian , Matioski Filho Gladyston Roberto , Godoi Lucas Dias , Vilela Capriotti Juan Rodolfo
Published: July 2020

Case:

We report the case of a patient who suffered traumatic avulsion of the gluteus medius and minimus tendons associated with posterior fracture-dislocation of the femoral head. The patient was treated with open reduction and internal fixation, followed by gluteus tenodesis with intraosseous anchors.

Conclusion:

Although in isolation, gluteus medius or gluteus minimus tendons tear, hip dislocation, and head fractures are relatively common injuries; the concurrence of these lesions is noteworthy for its rarity. This patient had an uneventful postoperative evolution, with a complete functional recovery, healing of the femoral head fracture and the tendons, and absence of signs of avascular necrosis.
Acute Hematogenous Osteomyelitis of the Scapula
Authors: Rizzi Andrew M. , Dickherber Jason L. , Bielski Robert
Published: July 2020

Case:

We present the case of a previously healthy 4-year-old boy with aggressive acute hematogenous osteomyelitis (AHO) of the scapula. Despite only 3 days of symptoms, he had a large abscess, prolonged bacteremia, and significant bony destruction. He required multiple debridements and intravenous antibiotics to control the infection but ultimately had full restoration of bony anatomy and normal function.

Conclusions:

Reported cases of AHO in the scapula are extremely rare. This case highlights the surgical approach to this problem and the importance of repeat advanced imaging and repeat debridements when clinically necessary.
A Quadruple-Porosity Model for Consistent Petrophysical Evaluation of Naturally Fractured Vuggy Reservoirs
Authors: Aboubacar Mahaman Salifou , Cai Zhongxian
Published: July 2020

Several dual- and triple-porosity models have been proposed for quantifying the porosity exponent (m) in multiporosity reservoirs. Total porosity (ϕ) is usually portioned into the matrix (ϕb) and vuggy porosity, which includes separate vugs (SVGs) and connected vugs (CVGs). As a result, in their majority, the existing petrophysical models were developed and applied mostly without any distinction between the various types of CVGs despite their specific pore geometries, which critically determine the properties of the rock/fluid systems. For instance, unlike otherwise CVGs, natural fractures (NFs) and microcracks that have low pore-aspect-ratio values are highly compressible; this can cause their closure and lead to increasing m values.

In this paper, we proposed a quadruple-porosity model that accounts for NFs (ϕ2 or ϕf) and CVGs (ϕc), in addition to ϕb and SVGs (ϕnc) separately, as distinct input variables to ensure accurate determination of m in composite reservoirs. The approach was based on the volume-model method and rules of electric-resistance networks in porous media. Computed water-saturation values used to validate the model show significant improvement and close agreement with the laboratory measurements, demonstrating the applicability of the proposed model for accurate prediction of m in naturally fractured vuggy reservoirs.

New correlations that consider the pore-type diversity were generated using a plot of ϕ vs. m, obtained with the proposed quadruple-porosity model. The procedure involved sorting the ϕ/m scattering points using pore-type mixing and relative abundance of specific porosity. It allowed defining consistent ϕ/m relationships, with determination coefficients of 0.7 to 0.9. This suggests that m varies with the pore-structure types; this was further demonstrated with a rock-frame flexibility factor (γ) used as a proxy to cluster the scattering points. The established correlations can alternatively be applied to reasonably predict m using detailed prior knowledge of pore-type description.
The statistical importance of a study for a network meta-analysis estimate
Authors: Rücker Gerta , Nikolakopoulou Adriani , Papakonstantinou Theodoros , Salanti Georgia , Riley Richard D. , Schwarzer Guido
Published: July 2020

Background: In pairwise meta-analysis, the contribution of each study to the pooled estimate is given by its weight, which is based on the inverse variance of the estimate from that study. For network meta-analysis (NMA), the contribution of direct (and indirect) evidence is easily obtained from the diagonal elements of a hat matrix. It is, however, not fully clear how to generalize this to the percentage contribution of each study to a NMA estimate. Methods: We define the importance of each study for a NMA estimate by the reduction of the estimate's variance when adding the given study to the others. An equivalent interpretation is the relative loss in precision when the study is left out. Importances are values between 0 and 1. An importance of 1 means that the study is an essential link of the pathway in the network connecting one of the treatments with another. Results: Importances can be defined for two-stage and one-stage NMA. These numbers in general do not add to one and thus cannot be interpreted as `percentage contributions'. After briefly discussing other available approaches, we question whether it is possible to obtain unique percentage contributions for NMA. Conclusions: Importances generalize the concept of weights in pairwise meta-analysis in a natural way. Moreover, they are uniquely defined, easily calculated, and have an intuitive interpretation. We give some real examples for illustration.
Association of glial and neuronal degeneration markers with Alzheimer‘s disease cerebrospinal fluid profile and cognitive functions
Authors: Teitsdottir Unnur D. , Jonsdottir Maria K. , Lund Sigrun H. , Darreh-Shori Taher , Snaedal Jon , Petersen Petur H.
Published: July 2020

Background

Neuroinflammation has gained increasing attention as a potential contributing factor in the onset and progression of Alzheimer‘s disease (AD). The objective of this study was to examine the association of selected cerebrospinal fluid (CSF) inflammatory and neuronal degeneration markers with signature CSF AD profile and cognitive functions among subjects at the symptomatic pre- and early dementia stages.

Methods

In this cross-sectional study, 52 subjects were selected from an Icelandic memory clinic cohort. Subjects were classified as having CSF AD (n=28, age=67, 33% female, Mini-mental state examination [MMSE]=28) or non-AD (n=24, age=70, 39% female, MMSE=27) profile based on the ratio between CSF total-tau (T-tau) and amyloid-β 1‐42 (Aβ 42 ) values (cut-off point chosen as 0.52). Novel CSF biomarkers included Neurofilament light (NFL), YKL-40, S100 calcium-binding protein B (S100B) and Glial fibrillary acidic protein (GFAP), measured with enzyme-linked immunosorbent assay (ELISA). Subjects underwent a neuropsychological assessment for evaluation of different cognitive domains including verbal episodic memory, non-verbal memory, language, processing speed and executive functions.

Results

Accuracy for distinguishing between the two CSF profiles was calculated for each CSF marker and cognitive domain. Verbal episodic memory performed the best overall (Area under curve [AUC]=0.80), with AUCs for CSF markers ranging from 0.61 to 0.64. For estimation of the relationships between CSF markers and cognitive domains (adjusted for age and education), Pearson‘s correlation and ridge regression analyses were performed. The ratio between NFL and YKL-40 levels correlated higher with verbal episodic memory score (r=-0.51, p <0.001) compared to single protein levels (NFL: r=-0.26, p =0.06; YKL-40: r=0.18, p =0.20). The correlation was also higher among those with CSF AD profile (r=-0.67, p <0.001) compared to those without (r=-0.46, p =0.03). GFAP levels showed weak correlation with executive functions scores (r=-0.37, p =0.007). Among those with a CSF AD profile, both S100B (r=-0.45, p =0.02) and GFAP (0.68, p <0.001) levels correlated with processing speed scores.

Conclusions

The novel CSF markers NFL, YKL-40 and GFAP show potential as markers for cognitive decline among individuals with core AD pathology at the symptomatic pre- and early stages of dementia.
Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue
Authors: Zhu Huihui , Ai Honglian , Hu Zhengrong , Du Dongyun , Sun Jie , Chen Ke , Chen Liang
Published: July 2020

Background: It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we investigated the possible molecular mechanisms of Cd detoxification process by comparative transcriptomic and metabolomic approaches. Results: The application of Sodium nitroprusside (SNP) as NO donor decreased the Cd content of tall fescue by 11% under Cd stress (T1 treatment), but the Cd content was increased by 24% when treated with Carboxy-PTIO (c-PTIO) together with Nitro-L-arginine methyl ester (L-NAME) (T2 treatment). RNA-seq analysis revealed that 904 (414 up- and 490 down-regulated) and 118 (74 up- and 44 down-regulated) DEGs were identified in the T1 vs Cd (only Cd treatment) and T2 vs Cd comparisons, respectively. Moreover, metabolite profile analysis showed that 99 (65 up- and 34-down- regulated) and 131 (45 up- and 86 down-regulated) metabolites were altered in the T1 vs Cd and T2 vs Cd comparisons, respectively. The integrated analyses of transcriptomic and metabolic data showed that 81 DEGs and 15 differentially expressed metabolites were involved in 20 NO-induced pathways. The dominant pathways were antioxidant activities such as glutathione metabolism, arginine and proline metabolism, secondary metabolites such as flavone and flavonol biosynthesis and phenylpropanoid biosynthesis, ABC transporters, and nitrogen metabolism.Conclusions: In general, the results revealed that there are three major mechanisms involved in NO-mediated Cd detoxification in tall fescue, including (a) antioxidant capacity enhancement; (b) accumulation of secondary metabolites related to cadmium chelation and sequestration; and (c) regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the NO-mediated cadmium stress response.
Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes
Authors: Peng Jiao , Zhao Yunlin , Dong Meng , Liu Shiquan , Hu Zhiyuan , Zhong Xiaofen , Xu Zhenggang
Published: July 2020

Background: The cultivated tea is one of the most important economic and ecological trees distributing worldwide. The cultivated tea suffered from long-term targeted selection of traits and overexploitation of habitats by human beings, which may change the genetic structure. Chloroplast is an organelle with a conserved cyclic structure, and can help us better understand the evolutionary relationship of Camellia plants.Results: The study conducted comparative analysis and evolution analysis between cultivated tea and wild tea, and detected the evolution characteristic in cultivated tea. Chloroplast genome sizes of cultivated tea were slightly different, ranged from 157,025 bp to 157,085 bp. These cultivated species were more conservative than wild species, in terms of the genome length, genes number, genes arrangement and GC contents. However, the IRs length of cultivated species was about 20 bp shorter than that of C. sinensis var. sisnensis. We also found that the nucleotide diversity of 14 sequences in cultivated tea was higher than that of wild tea. These results provided the evidence on the variation of chloroplast genomes of cultivated tea. Detail analysis on the chloroplast genome variation and evolution of cultivated tea showed that 67 SNPs and 46 indels and 16 protein coding genes had nucleotide substitutions. The most comment variation gene was ycf1. It has the largest number of nucleotide substitutions. At the same time, in ycf1, five amino acid sites were exhibiting site-specific selection, and a 9 bp sequence insertion was found in the C. sinensis cultivar. Anhua. The phylogenetic tree constructed by ycf1 sequence shows that two cultivated tea were not completely clustered, and the evolutionary relationship between C. sinensis var. sisnensis and C. sinensis cultivar. Longjing is closer than that of C. sinensis cultivar. Anhua.Conclusions: The cultivated species were more conservative than wild species in terms of architecture and linear sequence order. The variation of chloroplast genome of cultivated tea was mainly manifested in the nucleotide polymorphism of some sequences. The ycf1 gene played an important role in the adaptive evolution of cultivated tea. These results provided evidence regarding the influence of human activities on tea.
Examining the quality of record linkage process using nationwide Brazilian administrative databases to build a large birth cohort
Authors: Almeida Daniela , Gorender David , Ichihara Maria Yury , Sena Samila , Menezes Luan , Barbosa George C. G. , Fiaccone Rosimeire L. , Paixao Enny , Pita Robespierre , Barreto Mauricio L.
Published: July 2020

Background : Research using linked routine population-based data collected for non-research purposes has increased in recent years because they are a rich and detailed source of information. The objective of this study is to present an approach to prepare and link data from administrative sources in a middle-income country, to estimate its quality and to identify potential sources of bias by comparing linked and no-linked case. Methods: We linked two administrative datasets with data covering the period 2001 to 2015, using maternal attributes (name, age, date of birth, and municipally of residence) from Brazil: live birth information system and the 100 Million Brazilian Cohort (created using administrative records from over 114 million individuals whose families applied for social assistance via the Unified Register for Social Programmes) implementing an in house developed linkage tool CIDACS-RL. We then estimated the proportion of highly probably link and examined the characteristics of missed-matches to identify any potential source of bias. Results: A total of 27,699,891 live births linked with maternal information recorded in the baseline of the 100 Million Brazilian Cohort dataset of those, 16,447,414 (59.4%) children were found registered in the 100 Million Brazilian Cohort dataset. The proportion of highly probably link ranged from 39.3% in 2001 to 82.1% in 2014. A substantial improvement in the linkage after the introduction of maternal date of birth attribute, in 2011, was observed. Our analyses indicated a slightly higher proportion of missing data among missed matches and a higher proportion of people living in an urban area and self-declared as Caucasian among linked pairs when compared with non-linked sets. Discussion: We demonstrated that CIDACS-RL is capable of performing high quality linkage even with a limited number of common attributes, using indexation as a blocking strategy in larg e routine databases from a middle-income country. However, residual records occurred more among people under worse living conditions. The results presented in this study reinforce the need of evaluating linkage quality and when necessary to take linkage error into account for the analyses of any generated dataset.
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.
Authors: Dissanayake Duminda S.B. , Holleley Clare , Hill Laura , O’Meally D. , Deakin J. , Georges Arthur
Published: July 2020

Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results: We generated 96.7 x 10 9 150 bp paired-end genomic sequence reads from a XY male and 81.4 x 10 9 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions: The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi . Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
Transcriptome-based Selection and Validation of Optimal House-keeping Genes for Skin Research in Goats (Capra hircus)
Authors: Zhang Jipan , Deng Chengchen , Li Jialu , Zhao Yong-Ju
Published: July 2020

Background : In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat ( Capra hircus ) is an economically important livestock species and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology. Results: Based on the transcriptome dataset of 39 goat skin tissue samples, 8 genes ( SRP68 , NCBP3 , RRAGA , EIF4H , CTBP2 , PTPRA , CNBP , and EEF2 ) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes ( ACTB and GAPDH ) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was shown that NCBP3+SDHA+PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released. Conclusion: This study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3+SDHA+PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.
Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites
Authors: Song Jiali , Chen Changming , Zhang Shuanglin , Wang Juntao , Huang Zhubin , Chen Muxi , Cao Bihao , Zhu Zhangsheng , Lei Jianjun
Published: July 2020

Background: ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results: In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion: This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.
The Prevalence of Pathogenic Bacteria from Different Clinical Samples, Northern Part of Iraq.
Authors: MIYASAR ALLAA
Published: July 2020

Background Bacteria are prokaryotic which causes a wide range of diseases in human and animals as well, thus, early diagnosis of bacterial infection is an important step for their management. The vast majority of bacteria are harmless to human and some strains are even beneficial. However, some strains cause infections including pneumonia, meningitis and urinary tract infection…etc. The present study aimed to describe and determine the prevalence rate of pathogenic bacteria in different clinical samples from Duhok city, Kurdistan region of Iraq, as there are no available data of bacterial infections.Methods Totally, 200 adult patients enrolled in the present study during July 2017-July 2018. We collected different clinical specimens including (SFA, Bronchial Lavage, catheter, cerebrospinal fluid, body fluids, blood, semen, stool pus, urine, sputum and ear swabs). Standard microbiological techniques used for isolation and identification. All samples collected before antibiotic uses by specialized physician.Results The result reported that forty-six samples (23%) obtained from male and one hundred fifty-four samples (77%) obtained from females. A high diversity of pathogens was found but Staphylococcus aureus recorded the highest infection rate by (33.3%) which observed in 32 urine samples by and followed by E. coli (27.3%) and Coagulase-Negative Staphylococci (25.3%), which observed in 36 and 29 urine samples, respectively. Alternatively, Klebsiella, Streptococcus, Enterobacteriaceae and Pseudomonas aeruginosa were founded in few samples.Conclusion The highest diversity of potential pathogens observed in urine samples was E.coi. Over all, Staphlococcus aureus was predominant and recorded the highest prevalence rate by (33.3%) in 50 samples which followed by E. coli recorded in 41 samples (27.3%) and Coagulase-Negative Staphylococci observed in 38 samples (25.3%).
Molecular epidemiology and risk factors of Stenotrophomonas maltophilia infections in a Chinese teaching hospital
Authors: Duan Zhongliang , Qin Juanxiu , Liu Yao , Li Cui , Ying Chunmei
Published: July 2020

Background: Stenotrophomonas maltophilia ( S. maltophilia ) is an important opportunistic pathogen obtained in hospitals. With the abuse of broad spectrum antibiotics and invasive surgical devices, the rate of S . maltophilia infections is increasing every year. This study is an epidemiological analysis of the clinical and molecular characteristics of S . maltophilia infections in a Chinese teaching hospital. The goal is to obtain a comprehensive understanding of the status of S . maltophilia infections in order to provide strong epidemiological data for the prevention and treatment of S . maltophilia infections. Results: A total of 93 isolates from the Renji Hospital were included, in which 81 isolates were cultured from sputum samples, and 86 patients had underlying diseases. All of the patients had received antibiotic therapeutics. The multilocus sequence typing (MLST) analysis indicated that 61 different sequence types (STs) were found (including 45 novel STs), and the MLST did not show significantly dominant STs. The resistant rates to Trimethoprim/sulfamethoxazole (TMP/SMX) and levofloxacin were 9.7% and 4.3%. All of the strains were susceptible to minocycline. The positive rates of the four virulence genes Stmpr1 , Stmpr2 , Smf-1 , and Smlt3773 locus were 79.6%, 91.4%, 94.6% and 52.7%, respectively. The positive rates of the three biofilm genes rmlA , spgM, and rpfF were 82.8%, 92.5%, and 64.5%, respectively. The mean biofilm forming level of OD 492 was 0.54 ± 0.49, and there was no significant difference between different genders and age groups. Data from patients in the intensive care unit (ICU) and the control group were analyzed, and the independent risk factors of those who were infected in the ICU included immunosuppression and the increased of the use of antibiotics. Conclusions : Most of the patients had prior medical usage histories and baseline diseases. The carrying rate of virulence genes was high, the drug resistance rate of S . maltophilia was low, and the biofilm formation ability was strong. The increased use of antibiotics was an independent risk factor for S . maltophilia infection, which should receive more attention. No obvious clonal transmission was found in the same department.
Consolidating strategic information to monitor progress against the UNAIDS 90-90-90 targets: evaluating the operational feasibility of an electronic HIV testing register in Cape Town, South Africa
Authors: Jacob Nisha , Rice Brian , Kalk Emma , Heekes Alexa , Morgan Jennie , Brinkmann Samantha , Hargreaves James , Orgill Marsha , Boulle Andrew
Published: July 2020

Background HIV diagnosis in South Africa is based on a point-of-care testing (PoCT) algorithm with paper-based record-keeping. Aggregated testing data are reported routinely. To facilitate improved HIV case-based surveillance, the Western Cape Province implemented a unique pilot intervention to digitise PoCT results, at an individual level, and generate an electronic register using the newly developed Provincial Health Data Centre (PHDC). We describe the intervention (phased) and present an evaluation of the operational feasibility of the intervention. We also offer implementation insights into establishing electronic capture of individual level testing data. Methods Cross-sectional analyses were conducted on records of all patients attending a local Community Health Centre who had an HIV-PoCT during the study period. Data from the intervention were linked to the PHDC using a unique identifier and compared with aggregate data from the paper-based register. Correlation coefficients were calculated to quantify the correlation between the two monthly datasets. To support an understanding of the findings, the Department of Health project management team generated reflections on the implementation process, which were then grouped thematically into implementation lessons. Results In total, 11 337 PoCT records were digitised (70% (7954) during Phase I; and 30% (3383) during Phase II). Linkage of forms to the PHDC was 96% in Phase I and 98% in Phase II. Comparison with aggregate data showed high correlation during Phase I, but notable divergence during Phase II. Divergence in Phase II was due to stringent data quality requirements and high clinical staff turnover. Factors supporting implementation success in Phase I included direct oversight of data capturing by a manager with clinical and operational insight. Implementation challenges included operational, health system, and high cost-related issues. Conclusions We demonstrate that rapid digitisation of HIV PoCT data, without compromising currently collected aggregate data, is operationally feasible, and can contribute to person-level longitudinal HIV case-based surveillance. To take to scale, we will need to improve PoCT platforms and clerical and administrative systems. Although we highlight challenges, we demonstrate that electronic HIV testing registers can successfully replace manual registers and improve efforts to monitor and evaluate HIV testing strategies.
Albumin-bound paclitaxel and gemcitabine combination therapy in soft tissue sarcoma
Authors: Tian Zhichao , Zhang Fan , Li Po , Wang Jiaqiang , Yang Jinpo , Zhang Peng , Yao Weitao , Wang Xin
Published: July 2020

Background: The evidence that albumin-bound paclitaxel (nab-paclitaxel) is safe and efficacious for the treatment of many types of malignant tumors is continuously increasing. However, the clinical data and evidence of nab-paclitaxel and gemcitabine in metastatic soft tissue sarcoma (STS) treatment are rare.Methods: The data of 17 patients with metastatic STS who received nab-paclitaxel/ gemcitabine chemotherapy between January 2019 and February 2020 were retrospectively reviewed. All patients were treated with nab-paclitaxel/ gemcitabine only after doxorubicin-based chemotherapy had failed. We evaluated the median progression-free survival (m-PFS), disease control rate (DCR), objective response rate (ORR) and adverse events (AEs) in these patients. Results: The m-PFS was 6 months (95% CI, 2–9 months), ORR was 41.2% and DCR was 70.6%. The average change in target lesion diameter from baseline was -19.06±45.74%. While the majority of the treatment patients experienced grade 1 or 2 AEs, grade 3 or 4 AEs were not common, but included neutropenia (17.6%), fatigue (11.8%), anemia (11.8%), leukopenia (11.8%), nausea (5.9%), peripheral neuropathy (5.9%), diarrhea (5.9%), and thrombocytopenia (5.9%). No treatment-related deaths occurred. Conclusion: Nab-paclitaxel/ gemcitabine combination chemotherapy is comparatively effective in the treatment of STS, demonstrates low toxicity, and is worthy of further study.
PM2.5 exposure induced renal injury via the activation of the autophagic pathway in the rat and HK-2 cell
Authors: Huang Xiaoliu , Zhou Zhitong , Liu Xinwen , Li Jue , Zhang Lijuan
Published: July 2020

Background: Exposure to airborne fine particulate matter (PM2.5) has been declared to be harmful to human kidney. However, whether activation of the autophagic pathway plays key roles in the nephrotoxicity caused by PM2.5 exposure is still poorly understood. The aim of this study was to explore the mechanism of kidney damage after PM2.5 exposure in vivo and in vitro.Results: In the present study, statistically significant alterations in water intake, urine flow rate and mean blood pressure were observed between the concentrated PM2.5 (PM2.5) group and the filtered air (FA) group. Exposed animals showed severe edema of renal tubular epithelial cells, capillary congestion, reduction of the glomerular urinary space and early pro-fibrotic state. Moreover, significant increases in the levels of early kidney damage markers were observed in the exposed rats and these animals exhibited more apoptosis rate in kidney cells. In addition, PM2.5 exposure activated the autophagic pathway, as evidenced by LC3-I to LC3-II conversion, activation of P62 and beclin-1. All of these effects are in concurrence with the presence of more autophagosomes both in vivo and in vitro after PM2.5 exposure. Conclusions: Taken together, our findings indicated that PM2.5-induced renal function impairment via the activation of the autophagic pathway in renal tubular epithelial cells.