bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Similarity Searching System for Biological Phenotype Images Using Deep Convolutional Encoder-decoder Architecture
Authors: Wu Bizhi , Zhang Hangxiao , Lin Limei , Wang Huiyuan , Gao Yubang , Zhao Liangzhen , Chen Yi-Ping Phoebe , Chen Riqing , Gu Lianfeng 
Published: February 2019

Background:
The BLAST (Basic Local Alignment Search Tool) algorithm has been
widely used for sequence similarity searching. Analogously, the public phenotype images must be
efficiently retrieved using biological images as queries and identify the phenotype with high
similarity. Due to the accumulation of genotype-phenotype-mapping data, a system of searching
for similar phenotypes is not available due to the bottleneck of image processing.

Objective:
In this study, we focus on the identification of similar query phenotypic images by
searching the biological phenotype database, including information about loss-of-function and
gain-of-function.

Methods:
We propose a deep convolutional autoencoder architecture to segment the biological
phenotypic images and develop a phenotype retrieval system to enable a better understanding of
genotype–phenotype correlation.

Results:
This study shows how deep convolutional autoencoder architecture can be trained on
images from biological phenotypes to achieve state-of-the-art performance in a phenotypic images
retrieval system.

Conclusion:
Taken together, the phenotype analysis system can provide further information on the
correlation between genotype and phenotype. Additionally, it is obvious that the neural network
model of image segmentation and the phenotype retrieval system is equally suitable for any
species, which has enough phenotype images to train the neural network.
Gene Selection Method for Microarray Data Classification Using Particle Swarm Optimization and Neighborhood Rough Set
Authors: Ye Mingquan , Wang Weiwei , Yao Chuanwen , Fan Rong , Wang Peipei 
Published: February 2019

Background:
Mining knowledge from microarray data is one of the popular research
topics in biomedical informatics. Gene selection is a significant research trend in biomedical data
mining, since the accuracy of tumor identification heavily relies on the genes biologically relevant
to the identified problems.

Objective:
In order to select a small subset of informative genes from numerous genes for tumor
identification, various computational intelligence methods were presented. However, due to the
high data dimensions, small sample size, and the inherent noise available, many computational
methods confront challenges in selecting small gene subset.

Methods:
In our study, we propose a novel algorithm PSONRS_KNN for gene selection based on
the particle swarm optimization (PSO) algorithm along with the neighborhood rough set (NRS) reduction
model and the K-nearest neighborhood (KNN) classifier.

Results:
First, the top-ranked candidate genes are obtained by the GainRatioAttributeEval preselection
algorithm in WEKA. Then, the minimum possible meaningful set of genes is selected by
combining PSO with NRS and KNN classifier.

Conclusion:
Experimental results on five microarray gene expression datasets demonstrate that the
performance of the proposed method is better than existing state-of-the-art methods in terms of
classification accuracy and the number of selected genes.
Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea
Authors: Konda Aravind K. , Sabale Parasappa R. , Soren Khela R. , Subramaniam Shanmugavadivel P. , Singh Pallavi , Rathod Santosh , Chaturvedi Sushil K. , Singh Narendra P. 
Published: February 2019

Background:
Chickpea is a nutritional rich premier pulse crop but its production encounters
setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance.

Objective:
The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea
in response to herbicide stress and decipher their interacting partners.

Methods:
For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior
of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional
gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis
was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed
in chickpea using publicly available transcriptome data. Expression pattern of the identified gene
network was studied in chickpea-Fusarium interactions.

Results:
A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not
only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely
Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620,
Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes
based on the significant probability scores. Functional annotation indicated role in callose deposition and
response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in
wilt resistant and susceptible chickpea genotypes, infected with Fusarium.

Conclusion:
This is the first report of identification of a multi-stress responsive WRKY TF and its associated
GCN in chickpea.
Effect of Boswellia serrata on Rat Trachea Contractility In Vitro
Authors: Hewedy Wafaa Ahmed 
Published: February 2019

Background:
Boswellia serrata (family Burseraceae) has been traditionally used for the
treatment of a wide variety of diseases as arthritis, inflammatory bowel diseases, and airway diseases.
However, the direct bronchodilator efficacy of Boswellia serrata hasn’t been explored yet.

Objective:
We aimed at the present study to evaluate the direct effect of Boswellia serrata extract
(BSE) on isolated rat tracheal preparations precontracted with either Acetylcholine (ACh) or potassium
chloride (KCl).

Methods:
Tracheal rings were prepared from male Wistar rats (200-250 g). BSE (1-200 μg/ml) was
added to tracheal strips precontracted with either ACh or KCl and the response was observed. We
also investigated the consequences of epithelial denudation, indomethacin, and N-Nitro-L-arginine
on the relaxant effect of BSE as compared to that of the β-adrenoceptor agonist isoprenaline, or the
bitter taste receptor (TAS2R) agonist denatonium benzoate. Finally, the possible additive effects of
BSE to isoprenaline or denatonium-induced relaxation were evaluated.

Results:
By using a set of serial dosing and washout experiments with tracheal rings, results showed
that exposure to BSE resulted into a significant and concentration-dependent inhibitory effect on
airway smooth muscle contractions precontracted with either ACh or KCl. Epithelial denudation, indomethacin,
or N-Nitro-L-arginine had no significant effect on the obtained relaxation. Furthermore,
BSE potentiated the relaxant effect of isoprenaline on rat trachea.

Conclusion:
BSE exerts a direct concentration-dependent relaxant effect on precontracted tracheal
strips. These results could contribute towards validation of the traditional use of BSE in the treatment
of airway diseases.
Pengembangan Pembelajaran Penulisan Kreatif Berwawasan Lingkungangan Bidang Bahasa dan Sastra Indonesia bagi Guru dan Siswa Pondok Pesantren Muqimus Sunnah di Palembang
Authors: Dewojati Cahyaningrum 
Published: February 2019

One of the eﬀorts in supporting Sustainable Development Goals (SDGs) 2030 is noble moraleducation and environmental preservation through learning. In this case, creative writing is seen as an eﬀective learning medium to convey these values. Terefore, the development of environmentally sound creative writing study in the feld of language and Indonesian literature is considered necessary so that this community engagement activity is then implemented in Pondok Pesantren Muqimus Sunnah in Palembang. Te purpose of this community engagement is to improve the creativity of the community in the feld of creative writing that is environmentally sound as an eﬀort to support the Sustainable Development Goals (SDGs). Te method used in this community engagement is by delivering lectures on creative writing and training in both fction and nonfction. Games are also used as ways to covey the workshop materials. From this training, it seems that madrasah teacher and students are very enthusiastic and more eager to write. In conclusion, creative writing training that is embodied in games, as well as criticism of environmental conditions, is necessary to hone the criticality and creativity of the students and teachers in the world of literacy.
DA PENÍNSULA IBÉRICA À COLÔNIA BRASILEIRA: A CULTURA DO REISADO NUMA CIDADE DO SERTÃO DA BAHIA
Authors: Lopes Fernandes Adão , Dias de Carvalho Sousa Denise 
Published: February 2019

Este artigo traz os resultados de uma pesquisa realizada na Universidade do Estado da Bahia (UNEB), no Mestrado Profissional em Educação e Diversidade (MPED), no que diz respeito à presença da tradição cultural do terno de reis, de figuras e espadas nas práticas educativas dos/as professores/as do Colégio
Dom Antônio de Mendonça, em Genipapo, Saúde - BA. O estudo teve como objetivo rememorar o processo histórico da manifestação do reisado, especialmente, o terno de reis de figuras e espadas do povoado de Genipapo, enfatizando sua importância histórica, social e identitária para a cultura e a história local, bem como sua inserção dentro do contexto escolar da comunidade. Para tanto, retomamos os estudos de Morais Filho (1946), Querino (1914), Passarelli (2006) e Silva (2010). Quanto à metodologia, trata-se de uma abordagem qualitativa, pautada nos pressupostos teóricos da pesquisação. Nos instrumentos de obtenção e construção dos dados, realizamos uma revisão sistemática e de literatura, seguida de entrevistas semiestruturadas do tipo narrativa em oficinas pedagógico-culturais com sete professores/as. Esperamos com este estudo possibilitar um novo olhar acerca do percurso histórico do reisado, direcionando-o para as práticas educativas, transversalmente, a fim de responder a lacunas historicamente excludentes em relação à cultura popular e à história local, tendo em vista contribuir com o planejamento docente, desmitificando a visão urbanocêntrica de se pensar o currículo educacional que, atualmente, contribui para a descaracterização das tradições culturais locais, no sentido do
distanciamento das suas peculiaridades, vivências, contexto histórico e sociocultural.
IMAGENS DA/NA PESQUISA QUALITATIVA: A EXTENSA POSSIBILIDADE DE PESQUISAR IMAGES OF/IN QUALITATIVE RESEARCH: THE EXTENSIVE POSSIBILITY OF RESEARCH
Authors: PIATTI Célia Beatriz 
Published: February 2019

Resumo. Neste trabalho, entende-se que, entre tantos procedimentos selecionados para compor a metodologia de um estudo, utilizada na pesquisa qualitativa, a coleta de dados por meio da leitura de imagens paradas, utilizando-se da teoria semiótica é interessante e pode trazer um material rico para análise, uma vez que as imagens permitem ao pesquisador provocar no sujeito da pesquisa sensações, sentimentos, percepções de lugares e de pessoas para uma compreensão do objeto de estudo e seus matizes. Cabe ressaltar que a discussão referente ao uso de imagens nas pesquisas qualitativas envolve diferentes pontos a serem alvo de reflexão e debate, porém estamos, neste trabalho, abordando seu uso e valor na perspectiva de ampliar e oferecer outras formas de o sujeito pesquisado revelar questões que permeiam o campo em estudo. Palavras chave: Semiótica. Imagens. Pesquisas qualitativas. Abstract. In this work it is understood that among the many procedures selected to compose the methodology of a study used in qualitative research, the collection of data through the reading of still images using semiotics is interesting and can bring a rich material for analysis, since the images allow the researcher to provoke in the subject of the research sensations, feelings, perceptions of places and people for an understanding of the object of study and its nuances. It should be emphasized that the discussion regarding the use of images in qualitative research involves different points to be the subject of reflection and debate, however we are in this work, approaching its use and value in the perspective of expanding and offering other ways for the subject to reveal issues that permeate the field under study. Keywords: Semiotics. Images. Qualitative research.
SUR LA SEMIOTIQUE DES CULTURES DE FRANÇOIS RASTIER SOBRE A SEMIÓTICA DAS CULTURAS DE FRANÇOIS RASTIER
Authors: KURTS-WÖSTE Lia 
Published: February 2019

RESUMÉ. La sémiotique des cultures, héritière de Cassirer autant que du Saussure autographe, permet aujourd’hui de repenser la responsabilité des chercheurs dans les modélisations de leurs objets et de construire une interdisciplinarité exigeante. Elle démontre la puissance fédérative de la méthodologie des sciences de la culture et du premier structuralisme en exploitant ses principes critiques, historiques, comparatistes pour aborder aussi bien les objets culturels que les disciplines qui en rendent compte. L’activité scientifique herméneutique y est repensée dans sa dimension d’acte interprétatif responsable, en reconnectant de manière originale les sphères scientifiques, artistiques et éthico-politiques à travers l’exploration des points de convergence entre humanisme, humanité et Humanités. Mots-clés: sémiotique, linguistique, anthropologie, herméneutique, culture, œuvre (Rastier, Cassirer, Saussure) RESUMO. A semiótica das culturas, herdeira tanto de Cassirer quanto do autógrafo Saussure, hoje permite repensar a responsabilidade dos pesquisadores em modelar seus objetos e construir uma interdisciplinaridade exigente. Ela demonstra o poder federativo da metodologia das ciências da cultura e o primeiro estruturalismo, explorando seus princípios críticos, históricos e comparativos para abordar tanto os objetos culturais quanto as disciplinas que os explicam. A atividade científica hermenêutica é repensada em sua dimensão de ato interpretativo responsável, reconectando de forma original as esferas científica, artística e ético-política por meio da exploração dos pontos de convergência entre humanismo, humanidade e Humanidades. Palavras chave: Semiótica; linguística; antropologia; hermeneutica; cultura; obra (Rastier, Cassirer, Saussure).
Changes in Screening Practices for Prediabetes and Diabetes Since the Recommendation for Hemoglobin A1c Testing
Authors: Evron Joshua M. , Herman William H. , McEwen Laura N. 
Published: February 2019

OBJECTIVE
Screening involves the presumptive identification of asymptomatic individuals at increased risk for unrecognized disease. We examined changes in screening practices for prediabetes and diabetes since January 2010, when HbA1c was first recommended as an option for screening and diagnosis.

RESEARCH DESIGN AND METHODS
We studied members without diabetes of an HMO ≥45 years of age continuously enrolled for ≥3 years and assigned to primary care clinicians affiliated with a large academic health system. We defined screening as the first oral glucose tolerance test, HbA1c, or glucose test performed between 2010 and 2014.

RESULTS
Of 12,772 eligible patients, 9,941 (78%) were screened at least once over 3 years. HbA1c was the initial screening test 14% of the time and glucose 86% of the time. Of those screened with HbA1c, 63% had abnormal results defined as HbA1c ≥5.7% (≥39 mmol/mol). Of those tested with glucose, 30% had abnormal results defined as glucose ≥100 mg/dL, and 5% had abnormal results defined as glucose ≥126 mg/dL. Patients with abnormal HbA1c levels and those with glucose levels ≥126 mg/dL were equally likely to be scheduled for follow-up appointments (41% vs. 39%), but those with abnormal HbA1c levels were more likely to be diagnosed with prediabetes or diabetes (36% vs. 26%).

CONCLUSIONS
As we observed in 2004, rates of screening are high. HbA1c is still used less frequently than glucose for screening but is more likely to result in a clinical diagnosis. Evidence to support guidelines to define the role of random glucose screening, including definition of appropriate cut points and follow-up, is needed.
Association of Insulin Dose, Cardiometabolic Risk Factors, and Cardiovascular Disease in Type 1 Diabetes During 30 Years of Follow-up in the DCCT/EDIC Study
Authors: Braffett Barbara H. , Dagogo-Jack Samuel , Bebu Ionut , Sivitz William I. , Larkin Mary , Kolterman Orville , Lachin John M. 
Published: February 2019

OBJECTIVE
The Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) study demonstrated the beneficial effects of intensive therapy on atherosclerosis and clinical cardiovascular disease (CVD) outcomes. The current analyses evaluated the relationship between longitudinal changes in insulin dose and CVD risk factors and outcomes.

RESEARCH DESIGN AND METHODS
A total of 1,441 participants were randomly assigned to intensive or conventional diabetes therapy during the DCCT. After an average of 6.5 years of follow-up, 96% of the surviving cohort enrolled in the EDIC observational study, which included annual visits with detailed medical history, physical examination, and laboratory testing. CVD events were adjudicated by a review committee. Generalized linear mixed models and Cox proportional hazards regression models were used to assess the association between insulin dose and cardiometabolic risk factors and CVD risk, respectively, over a total of 30 years.

RESULTS
Higher insulin doses were significantly associated with a less favorable cardiometabolic risk profile (higher BMI, pulse rate, and triglycerides and lower HDL cholesterol) with the exception of lower diastolic blood pressure and lower LDL cholesterol. In a minimally adjusted model, a 0.1 unit/kg body wt/day increase in insulin dose was associated with a 6% increased risk of any CVD (95% CI 3, 9). However, the association with insulin dose was no longer significant after adjustment for other CVD risk factors.

CONCLUSIONS
During DCCT/EDIC, higher insulin doses were associated with adverse trends in several cardiometabolic risk factors, even after multivariable adjustment, but not with incident CVD outcomes.
Association of Diabetes and Glycated Hemoglobin With the Risk of Intracerebral Hemorrhage: A Population-Based Cohort Study
Authors: Saliba Walid , Barnett-Griness Ofra , Gronich Naomi , Molad Jeremy , Naftali Jonathan , Rennert Gad , Auriel Eitan 
Published: February 2019

OBJECTIVE
To examine the association of diabetes and glycated hemoglobin (HbA1c) with the risk of intracerebral hemorrhage (ICH) in a large population-based cohort.

RESEARCH DESIGN AND METHODS
The computerized database of the largest health care provider in Israel was used to identify adult members aged 40 years or older and alive at 1 January 2010 (297,486 with diabetes and 1,167,585 without diabetes). The cohort was followed until 31 December 2017 for incidence of ICH. Multivariable Cox proportional hazards regression models, adjusted for baseline disease risk score, were applied to estimate the hazard ratio (HR) of ICH.

RESULTS
Overall 4,170 ICH cases occurred during 10,730,915 person-years of follow-up. Diabetes was independently associated with increased ICH risk, with hazard ratio (HR) 1.36 (95% CI 1.27–1.45), and increased with longer diabetes duration: 1.23 (1.12–1.35) and 1.44 (1.34–1.56) for diabetes duration ≤5 years and &gt;5 years, respectively. The increased ICH risk associated with diabetes was more pronounced in patients ≤60 years old (Pinteraction &lt;0.001). Among patients with diabetes, HbA1c had a nonlinear J-shaped relationship with ICH (P for nonlinearity = 0.0186). Compared to the fourth HbA1c decile, 6.5–6.7% (48–50 mmol/mol), the HR for ICH was 1.27 (1.01–1.59) and 2.19 (1.75–2.73) in the lowest HbA1c decile, ≤6.0% (≤42 mmol/mol), and highest HbA1c decile, &gt;9.3% (&gt;78 mmol/mol), respectively.

CONCLUSIONS
Diabetes is associated with increased risk of ICH that is directly associated with diabetes duration. ICH and HbA1c appear to have a J-shaped relationship, suggesting that both poor control as well as extreme intensive diabetes control might be associated with increased risk.
KAJIAN VALUASI EKONOMI WANA WISATA TAMAN HUTAN BERDASARKAN PENDAPAT MASYARAKAT PENGUNJUNG
Authors: Yustiani Yonik Meilawati , E Emilia , Permana Asep 
Published: February 2019

Kajian ini bertujuan untuk menilai secara ekonomi karakteristik Taman Hutan Gunung Tangkuban Perahu sebagai objek wisata. Metode yang digunakan pada studi ini adalah menggunakan pendekatan Travel Cost Method atau yang dikenal dengan Metode Biaya Perjalanan, yang prinsipnya menggunakan biaya perjalanan untuk menghitung nilai permintaan rekreasi suatu sumber daya alam yang tidak memiliki harga pasar. Kajian ini menghasilkan suatu persamaan yang mengindikasikan bahwa semakin tinggi pendapatan rata-rata per kapita, maka permintaan rekreasi juga akan semakin besar serta semakin tinggi biaya perjalanan akan menyebabkan berkurangnya jumlah pemintaan. Berdasarkan analisis kurva permintaan diperoleh indikasi bahwa pada tingkat harga tiket sebesar Rp 5000 maka diperoleh penerimaan sebesar Rp 59.511.050,00. Penerimaan akan mencapai optimum pada harga tiket sebesar Rp 8.000 yakni sebesar Rp 69.416.080,00 dengan tidak mengabaikan fungsi sosial dan pendidikan harga tiket yang masuk sebenarnya bisa di tetapkan tidak setinggi dimana penerimaan mencapai optimum sehingga kawasan hutan wisata dapat berjalan dengan selaras dengan berbagai golongan masyarakat.
PENGEMBANGAN BUKU AJAR TEMATIK BERVISI SETS UNTUK MENANAMKAN KONSEP SUSTAINABLE AND RENEWABLE ENERGY SISWA SEKOLAH DASAR
Authors: Atmojo Setyo Eko , Kurniawati Wahyu 
Published: February 2019

Penelitian ini bertujuan untuk mengembangkan buku ajar tematik bervisi science, environment, technology and society (SETS) untuk menanamkan konsep sustainable and renewable energy siswa sekolah dasar. Penelitian ini merupakan penelitian pengembangan (Research and Development). Pengembangan dilakukan pada buku ajar untuk siswa kelas III Sekolah Dasar dengan tema energi kemudian buku ajar tersebut divalidasikan untuk selanjutnya direvisi dan diimplemantasikan. Selama uji coba, dilakukan pengamatan aktivitas siswa, pemberian angket ketepatan pembelajaran dan soal tes untuk mengetahui penguasaan konsep sustainable and renewable energy. Hasil penelitian menunjukkan bahwa tingkat kevalidan buku ajar sebesar 4,26 yang berada pada kategori valid. Kemampuan penguasaan konsep sustainable and renewable energy berada pada level baik, aktivitas siswa berada pada kategori baik yaitu lebih dari 70 % siswa aktif. Guru dan siswa juga memberikan positif terhadap hasil pengembangan buku ajar.
RELASI GENDER DALAM PENGAMBILAN KEBIJAKAN STRATEGIS PARTAI PADA PARTAI ISLAM
Authors: Sastrawati Nila 
Published: February 2019

Sistem internal partai tidak terlepas dari relasi yang terbangun antara identitas perempuan dan identitas laki-laki. Bryan menjelaskan bahwa dalam teori sosialisasi, perbedaan laki-laki dan perempuan dibentuk oleh variasi budaya, dan dalam analisis conversational menunjukkan perbedaan dalam pola gangguan percakapan antara laki-laki dan perempuan yang bermuatan penggunaan kekuatan. Di dalam organisasi dimana laki-laki dan perempuan memperjuangkan sebuah kekuasaan, komunikasi yang terjalin tetap mengandung muatan kekuasaan laki-laki. Dalam konteks ini, postmodernism menempatkan lakilaki dan perempuan dengan “ide identitas laki-laki yang plural” dan ide identitas perempuan yang plural”, bukan pada tataran “kesamaan laki-laki dan perempuan”.