bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of the transcriptomes of two rice subspecies reveals differentially expressed genes associated with phenotypic differences and reproductive isolation
Authors: pang hongbo , Wang Junrui , Chen Qiang , Li Jiaqi , Li Yueying , Wu Longkun , Yang Qingwen , Zheng Xiaoming 
Published: December 2019

Abstract
Background: Rice has been used as a model plant to study adaptation, genome evolution and reproductive isolation among species and the genetics and evolution of complex traits. Two subspecies of cultivated rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. Results: To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica plants, and identified 97,005 transcribed fragments and 7702 novel transcriptionally active regions. We also identified 1857 (4.58% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. According to previous population genetic analyses, these DEGs may associate with the phenotypic differences between the two subspecies. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′ flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs.Conclusion: This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs that may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.
Enhancing Xanthine Dehydrogenase Activity is an Effective Way to Delay Leaf Senescence and Increase Rice Yield
Authors: Han Ruicai , He Xunfeng , Pan Xiaohua , Shi Qinghua , Wu Ziming 
Published: December 2019

Abstract
Xanthine dehydrogenase (XDH) is an important enzyme in purine metabolism. It is involved in regulation of the normal growth and non-biological stress-induced ageing processes in plants. The present study investigated XDH’s role in regulating rice leaf senescence. We measured physical characteristics, chlorophyll content and fluorescence parameters, active oxygen metabolism, and purine metabolism in wild-type Kitaake rice ( Oryza sativa L.), an OsXDH over-expression transgenic line ( OE9 ), and an OsXDH RNA interference line ( Ri3 ) during different growth stages. The expression patterns of the OsXDH gene confirmed that XDH was involved in the regulation of normal and abiotic stress-induced ageing processes in rice. There was no significant difference between the phenotypes of transgenic lines and wild type at the seedling stage, but differences were observed at the full heading and maturation stages. The OE9 plants were taller, with higher chlorophyll content, and their photosystems had stronger light energy absorption, transmission, dissipation, and distribution capacity, which ultimately improved the seed setting rate and 1000-seed weight. The opposite effect was found in the Ri3 plants. The OE9 line had a strong ability to remove reactive oxygen species, with increased accumulation of allantoin and alantoate. Experimental spraying of allantoin on leaves showed that it could alleviate chlorophyll degradation and decrease the content of H 2 O 2 and malonaldehyde (MDA) in rice leaves after the full heading stage. The urate oxidase gene ( UO ) expression levels in the interference line were significantly lower than those in the over-expression line and wild-type lines. The allantoinase ( ALN ) and allantoate amidinohydrolase ( AAH ) genes had significantly higher expression in the Ri3 plants than the in OE9 or wild-type plants, with OE9 plants showing the lowest levels. The senescence-related genes ACD1 , WRKY23 , WRKY53 , SGR , XERO1 , and GH27 in Ri3 plants had the highest expression levels, followed by those in the wild-type plants, with OE9 plants showing the lowest levels. These results suggest that enhanced activity of XDH can regulate the synthesis of urea-related substances, improve plant antioxidant capacity, effectively delay the ageing process in rice leaves, and increase rice yield.
Evaluating the efficacy of a low-cost, minimally-invasive cognitive MRI targeted biopsy protocol in the Prostate Imaging Reporting and Data System (PI-RADS) version 2 era.
Authors: Takeshima Yuta , Tanaka Yoshinori , Takemura Kotaro , Nakazono Shusaku , Yamashita Eiko , Kume Haruki 
Published: December 2019

Abstract
Background: New MRI-guided targeting biopsy methods have increased cancer yield of prostate biopsies. However, cost and time constraints have made it difficult for many institutions to implement these newer methods. We evaluated the diagnostic performance of a low-cost, minimally-invasive, cognitive MRI-targeted biopsy protocol based on 1.5T multiparametric MRI graded with Prostate Imaging Reporting and Data System version 2 that is easily implemented in any low- to intermediate- volume center. Methods: Retrospective analysis of 255 patients who underwent prostate biopsy between December 2016 and March 2019 at a single facility. Indication for biopsy was based on clinical parameters including 1.5T multiparametric MRI. In addition to 10-core systematic biopsy, targeted cores were obtained with cognitive recognition under ultrasound. A control group of 198 patients biopsied without prior MRI from January to December 2015 was also analyzed. Results: Prostate biopsy preceded by MRI had a significantly higher probability of detecting both prostate cancer (68.1% vs. 43.6%) and clinically significant cancer (56.2% vs. 29.4%) (p values< 0.01). Combination of systematic biopsy and targeted biopsy outperformed either regimen alone for detection of prostate cancer. Multivariate analysis showed PSA density and prostate imaging reporting and data system score were independent risk factors of prostate cancer. A proposed diagnostic model showed sensitivity of 88.6%, specificity of 55%, PPV of 81.2%, NPV of 68.8%, and accuracy of 78%. Prostate imaging reporting and data system score was correlated with a higher presence of prostate cancer, clinically significant prostate cancer, and a higher pathological grade. Conclusions: Incorporation of pre-biopsy MRI imaging, scoring, and targeted biopsy improved cancer yield and achieved diagnostic performance comparable to newer methods of higher cost. Future alterations of possible benefit included increasing the number of target cores per lesion, and combining prostate imaging reporting and data system score and PSA density as indicators for biopsy.
Echocardiographic evidence of left ventricular untwisting-filling interplay
Authors: Hodzic Amir , Garcia Damien , Saloux Eric , Ribeiro Paula A.B. , Ethier Amélie , Thomas James D. , Milliez Paul , Normand Hervé , Tournoux Francois 
Published: December 2019

Abstract
Background: Left ventricular untwisting generates an early diastolic intraventricular pressure gradient (DIVPG) than can be quantified by echocardiography. We sought to confirm the quantitative relationship between peak untwisting rate and peak DIVPG in a large adult population.Methods: From our echocardiographic database, we retrieved all the echocardiograms with a normal left ventricular ejection fraction, for whom color Doppler M-Mode interrogation of mitral inflow was available, and left ventricular untwisting rate was measurable using speckle tracking. Standard indices of left ventricular early diastolic function were assessed by Doppler (peaks E, e’ and Vp) and speckle tracking (peak strain rate Esr). Load dependency of DIVPG and untwisting rate was evaluated using a passive leg raising maneuver. Results: We included 154 subjects, aged between 18 to 77 years old, 63% were male. Test-retest reliability for color Doppler-derived DIVPG measurements was good, the intraclass correlation coefficients were 0.97 [0.91-0.99] and 0.97 [0.67-0.99] for intra- and inter-observer reproducibility, respectively. Peak DIVPG was positively correlated with peak untwisting rate (r = 0.73, P < 0.001). On multivariate analysis, peak DIVPG was the only diastolic parameter that was independently associated with untwisting rate. Age and gender were the clinical predictive factors for peak untwisting rate, whereas only age was independently associated with peak DIVPG. Untwisting rate and DIVPG were both load-dependent, without affecting their relationship. Conclusions: Color Doppler-derived peak DIVPG was quantitatively and independently associated with peak untwisting rate. It thus provides a reliable flow-based index of early left ventricular diastolic function.
Kids in a Candy Store: An objective analysis of children's interactions with food in convenience stores
Authors: McKerchar Christina , Smith Moira , Gage Ryan , Williman Jonathan , Abel Gillian , Lacey Cameron , Mhurchu Cliona Ni , Signal Louise 
Published: December 2019

Abstract
Background: Increasing rates of childhood obesity worldwide has focused attention on the obesogenic food environment and how it influences dietary behaviour and bodyweight in children. The neighbourhood convenience store is a key setting in children’s food environments. The Kids’Cam study enabled the objective measurement of the world in which children live. This paper reports on an analysis of children’s interaction with food in convenience stores.Methods: Kids’Cam NZ was a cross-sectional study conducted from July 2014 to June 2015 in the Wellington region of New Zealand, in which 168 randomly selected children aged 11-14 years old wore a wearable camera for a 4-day period. The camera captured a 136° image of the children’s surroundings every seven seconds. In this ancillary study, ‘Kids’Cam Convenience Stores’, images from children who visited a convenience store were manually coded for food and drink availability, marketing, purchase and consumption. Results: Twenty-two percent of children (n=37) visited convenience stores on 62 occasions during the 4-day data collection period. Non-core items dominated the food and drinks available to children in convenience stores at a rate of 8.3 to 1 (means, 300 non-core and 36 core, respectively). The food and drinks marketed in-store were overwhelmingly non-core, and promoted using accessible placement, price offers, product packaging, and signage. Most of the 70 items purchased by children were non-core foods or drinks (94.6%) and all of the purchased food or drink subsequently consumed by children was non-core. Confectionary and sugary drinks were the items most frequently purchased and consumed. Conclusions: This research highlights convenience stores as a key source of unhealthy food and drink for children, where unhealthy food and drinks are marketed, available, and subsequently purchased and consumed. Policies are urgently needed to reduce the role of convenience stores in the obesogenic food environment in which children live.
Development and application of loop-mediated isothermal amplification label-based nanoparticles lateral flow biosensor for detection of Mycobacterium tuberculosis
Authors: Wang Xingyun , Wang Yi , Jiao Weiwei , Wang Guirong , Wang Yacui , Quan Shuting , Qi Hui , Sun Lin , Shen Chen , Li Jieqiong , Huang Hairong , Shen Adong 
Published: December 2019

Abstract
Tuberculosis is a serious disease with high morbidity and mortality, thus rapid and cost-effective diagnostic test for Mycobacterium tuberculosis (MTB) is urgently needed. Here, a novel detection diagnostic technique, termed as loop-mediated isothermal amplification label-based nanoparticles with lateral flow biosensor (LAMP-LFB), was developed and evaluated for rapid, reliable and objective detection of MTB. Two sets of primers, which targeted IS 6110 and IS 1081 sequences of MTB, were simultaneously designed for establishment of LAMP-LFB assay. The optimal reaction conditions of MTB-LAMP-LFB assay confirmed were 66ºC for only 50min. The analytical sensitivity of MTB-LAMP-LFB is 10fg of genomic templates in pure culture, and the detection results obtained from LFB was in conformity with agarose gel electrophoresis. No cross-reactivity with other common bacteria and non-tuberculous mycobacteria strains (NTM) was obtained. A total of 158 clinical samples were collected from presumptive 158 TB patients, were used for evaluating the feasibility of MTB-LAMP-LFB assay. Among 98 TB patients diagnosed with composite reference standard, the positive rate for MTB detection using liquid culture, Xpert MTB/RIF and LAMP-LFB were 40.0% (39/98), 50.0% (48/98), and 86.7% (85/98), respectively. Among 39 culture confirmed samples, 84.6% (33/39) cases were Xpert MTB/RIF-positive and 92.3% (36/39) were LAMP-LFB-positive. For the 59 clinically diagnosed TB cases 25.4% (15/59) and 83.0% (49/59) were Xpert MTB/RIF-positive and LAMP-LFB positive, respectively. Therefore, MTB-LAMP-LFB assay is a simple, reliable, and sensitive method for MTB detection and maybe prospective in early diagnosis of MTB.
Aspirin for metal stent in malignant distal common bile duct obstruction (AIMS): Study protocol for a multicenter randomized controlled trial
Authors: Choi Jin Ho , Paik Woo Hyun , You Min Su , Lee Kyong Joo , Choi Young Hoon , Shin Bang-sup , Lee Sang Hyub , Ryu Ji Kon , Kim Yong-Tae 
Published: December 2019

Abstract
Background Endoscopic retrograde biliary drainage (ERBD) is the treatment of choice for patients with malignant distal common bile duct (CBD) obstruction. Self-expandable metal stents (SEMS), which are commonly used in unresectable cases, have many clinical advantages, including longer stent patency. Although the expected patency of SEMS is around eight months, it has recently been reported that the duration of SEMS patency in patients using aspirin is prolonged. Our study therefore aims to confirm the effect of aspirin on SEMS patency. Methods This is an investigator-initiated, prospective, multicenter, double-blind, randomized placebo-controlled trial that will be conducted from November 2017 in four tertiary centers in South Korea. We intend to include in our study 184 adult (≥ 20 years) patients with malignant distal CBD obstruction for whom ERBD with SEMS was successfully performed. The patients will be randomly allocated to two groups, which will comprise patients who have either taken 100 mg aspirin or a placebo for six months after index ERBD. The primary outcome will be the rate of stent dysfunction, and the secondary outcomes will be the duration of patency, the rate of reintervention, and the occurrence of adverse events. Discussion The aspirin for metal stents in malignant distal common bile duct obstruction (AIMS) study will determine the efficacy of aspirin in maintaining metal stent patency in patients with malignant distal CBD obstructive.
Transmissão do diagnóstico de câncer sob a perspectiva da observação psicológica
Authors: Silva Tamires Daiane da , Foger Débora , Pizato Elaine Cristina Gardinal , Santos Paulo Sérgio da Silva 
Published: December 2019

Introdução: A transmissão do diagnóstico de câncer pode gerar ansiedade e nervosismo no indivíduo, por não saber lidar com essa situação, assim, o indivíduo entende como se a morte fosse o único desfecho nessa situação. Objetivo: observar como a pessoa com câncer e seus familiares se comportaram no momento do diagnóstico. Materiais e métodos: Para realizar este estudo, utilizou-se o relato de caso para avaliar como o paciente e seus familiares receberam informações sobre o diagnóstico de câncer. O procedimento utilizado foi a observação não participante, pois com ela foi possível descrever os dados e comportamentos expostos em um determinado momento. Resultados: Por meio da observação, ficou claro o quanto o diagnóstico de câncer sacode a estrutura familiar, uma vez que a doença se refere ao sinônimo de morte. Conclusões: foi possível observar os comportamentos em uma situação difícil, que é receber um diagnóstico de câncer. Com este estudo, os pontos comuns entre o que foi observado e o que a literatura traz sobre a transmissão do diagnóstico de câncer, como medo e ansiedade, foram percebidos.Descritores: Neoplasias; Diagnóstico Bucal; Psicologia; Observação.ReferênciasYamaguchi NH. O câncer na visão da oncologia. In: Carvalho MMMJ. Introdução à Psiconcologia. Campinas: Livro Pleno; 2003.Gimenes MGG. Definição, foco de estudo e intervenção. In: Carvalho MMMJ. Introdução à Psiconcologia. Campinas: Livro Pleno; 2003.Carvalho MMMJ. Psico-Oncologia: história, características e desafios. Psicologia USP. 2002;13:151-66.World Halth Organization (WHO). The World Health Organization’s fight against cancer: strategies that prevent, cure and care. 2007.Farinhas GV, Wendling MS, Dellazzana-Zanon LL. Impacto psicológico do diagnóstico de câncer na família: um estudo de caso a partir da percepção do cuidador. Pensando Fam. 2013;17: 111-29. Landskron LMF. Psicooncologia: as descobertas sobre o câncer ao longo da história. In: Hart CFM. Câncer: uma abordagem psicológica. Porto Alegre: AGE; 2008.Silva VCE, Fontão Zago MM. A revelação do diagnóstico de câncer para profissionais e pacientes. Rev Bras Enferm. 2005;58:476-80.Carvalho MMMJ. O sofrimento da dor em câncer. In: Carvalho MMMJ. Introdução à Psiconcologia. Campinas: Livro Pleno. 2003.Scorsolini-Comin F, Vilela e Sousa L, Santos MA. Tornanr-se psicólogo: experiência de estágio de Psico-Oncologia em equipe multiprofissional de saúde. Rev bras orientac prof. 2008;9(2):113-25.Donna MF, Matos MA. A necessidade da observação em ciência. In: Donna MF, Matos MA. Ensinando observação: uma introdução. 4. ed. São Paulo: Edicon; 1999.
The Predicted Effect of Projected Climate Change on the Economics of Conservation Tillage
Authors: Hodde Whitney , Sesmero Juan , Gramig Benjamin , Vyn Tony , Doering Otto 
Published: December 2019

We evaluate the economics of conservation tillage (chisel till and no till) and examine the impact of projected climate change on the economic attractiveness of reduced tillage practices. We use data from a long‐term (39‐yr) field experiment in Indiana to estimate yield response functions describing the relationship between tillage practices and corn (Zea mays L.) and soybean (Glycine max L.) yields in poorly drained (but systematically tile‐drained) soils, and the mediating role of weather and crop rotation on that relationship. We subsequently couple estimated yield functions with stochastic simulations of weather variables under current and projected climatic regimes to construct distributions describing the probability that conservation tillage will result in higher profits than more intensive tillage under alternative crop rotations. We calculate the subsidy, if needed, that would make a risk‐neutral farmer indifferent between conservation and intensive tillage practices under alternative climatic regimes. A key finding of this study is that projected climate change enhances the economics of conservation tillage, thereby substantially reducing the economic hurdle required to induce its adoption in the study area. The framework developed and demonstrated can be applied to areas with different soils and growing conditions to examine the economics of conservation tillage under current and future climate.Core Ideas

We examine effect of climate change on economics of reduced tillage.
We use data from a long‐term field experiment in Indiana
We calculate probability that reduced till will result in higher profit
Projected climate change enhances the economics of conservation tillage
Climate change may substantially reduce subsidies required for adoption
Self-optimizer data-mining method for aquifer level prediction
Authors: Bozorg-Haddad Omid , Delpasand Mohammad , Loáiciga Hugo A. 
Published: December 2019

Abstract
Groundwater management requires accurate methods for simulating and predicting groundwater processes. Data-based methods can be applied to serve this purpose. Support vector regression (SVR) is a novel and powerful data-based method for predicting time series. This study proposes the genetic algorithm (GA)–SVR hybrid algorithm that combines the GA for parameter calibration and the SVR method for the simulation and prediction of groundwater levels. The GA–SVR algorithm is applied to three observation wells in the Karaj plain aquifer, a strategic water source for municipal water supply in Iran. The GA–SVR's groundwater-level predictions were compared to those from genetic programming (GP). Results show that the randomized approach of GA–SVR prediction yields R2 values ranging between 0.88 and 0.995, and root mean square error (RMSE) values ranging between 0.13 and 0.258 m, which indicates better groundwater-level predictive skill of GA-SVR compared to GP, whose R2 and RMSE values range between 0.48–0.91 and 0.15–0.44 m, respectively.
Recognition of Fungal Components by the Host Immune System
Authors: García-Carnero Laura C. , Martínez-Álvarez José A. , Salazar-García Luis M. , Lozoya-Pérez Nancy E. , González-Hernández Sandra E. , Tamez-Castrellón Alma K. 
Published: December 2019

:By being the first point of contact of the fungus with the host, the cell wall plays an important role in the pathogenesis, having many molecules that participate as antigens that are recognized by immune cells, and also that help the fungus to establish infection. The main molecules reported to trigger an immune response are chitin, glucans, oligosaccharides, proteins, melanin, phospholipids, and others, being present in the principal pathogenic fungi with clinical importance worldwide, such as Histoplasma capsulatum, Paracoccidioides brasiliensis, Aspergillus fumigatus, Candida albicans, Cryptococcus neoformans, Blastomyces dermatitidis, and Sporothrix schenckii. Knowledge and understanding of how the immune system recognizes and responds to fungal antigens are relevant for the future research and development of new diagnostic tools and treatments for the control of mycosis caused by these fungi.
Measurement of Iron Content and Detection of Sulfate Ion in Traditional/ Industrial Canned Black Olives in Iran
Authors: Asadi-Sharifi Tayebeh , Peivasteh-Roudsari Leila , Molaee-Aghaee Ebrahim , Nazmara Shahrokh , Sadighara Parisa , Khaneghah Amin M. 
Published: December 2019

Background:
Black olive contains considerable concentrations of phenolic compounds,
which can result in a higher antioxidant component compared with green olives. Sometimes, as food
fraud, the use of unwanted substances has been observed such as iron sulfate or iron particles for
blackening olives, eventually causing adverse effects on the tissues of the digestive tract, brain, kidney,
and liver in the consumer. The main purpose of this study was to determine flavonoids, iron
content and ion sulfate in canned black olives.

Methods:
Canned black olive from inland/imported and traditional/industrial samples were collected.
The amount of iron, sulfate ion, and flavonoids content were measured by ICP-OES and
spectrophotometer, respectively.

Results:
Industrial black olives (brand N) from Turkey showed the highest iron content (110.17 mg/kg)
and traditional black olives purchased from Rudbar, showed the lowest iron content (6.72 mg/kg).
These values were lower than the iron limit in canned black olives (150 mg/kg). The highest and
lowest levels of sulfate were also found in the traditional black olive of Rudbar and industrial black
olives of Greece, respectively. Sulfate amount was determined between 23.225-82.102 mg/kg.
Traditional black olives of Roudbar had the highest flavonoid, and the lowest flavonoid content was
shown by the industrial black olive of Turkey. The pH was in the range of 4.4-4.8, indicating that the
pH of any of the samples was not higher than the standard maximum level.

Conclusion:
According to the results of this study, iron sulfate has not been added intentionally to
the collected samples.