bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography
Authors: Teramoto Shota , Takayasu Satoko , Kitomi Yuka , Arai-Sanoh Yumiko , Tanabata Takanari , Uga Yusaku 
Published: March 2020

Abstract
Background: X-ray computed tomography (CT) allows us to visualize root system architecture (RSA) beneath the soil, non-destructively and in a three-dimensional (3-D) form. However, CT scanning, reconstruction processes, and root isolation from X-ray CT volumes, take considerable time. For genetic analyses, such as quantitative trait locus mapping, which require a large population size, a high-throughput RSA visualization method is required. Results: We have developed a high-throughput process flow for the 3-D visualization of rice (Oryza sativa) RSA (consisting of radicle and crown roots), using X-ray CT. The process flow includes use of a uniform particle size, calcined clay to reduce the possibility of visualizing non-root segments, use of a higher tube voltage and current in the X-ray CT scanning to increase root-to-soil contrast, and use of a 3-D median filter and edge detection algorithm to isolate root segments. Using high-performance computing technology, this analysis flow requires only 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing, to visualize rice RSA. This reduced time allowed us to conduct the genetic analysis associated with 3-D RSA phenotyping. In 2-week-old seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively. The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth. Using the developed process flow, we were able to follow daily RSA development, i.e., 4-D RSA development, of an upland rice variety, over three weeks. Conclusions: We developed a high-throughput process flow for 3-D rice RSA visualization by X-ray CT. The X-ray dose assay on plant growth has shown that this methodology could be applicable for 4-D RSA phenotyping. We named the RSA visualization method ‘RSAvis3D’ and are confident that it represents a potentially efficient application for 3-D RSA phenotyping of various plant species.
Untreated dental caries prevalence and impact on the quality of life among 11 to 14-year-old Egyptian schoolchildren: A cross-sectional study
Authors: Eid Samar , Khattab Nagwa , Elheeny Ahmad 
Published: March 2020

Abstract
Background This study aimed to assess caries prevalence and experience among 11 to 14 years, school children, analyze demographic, socioeconomic, personal and professional dental care in relation to untreated carious lesions, and evaluates the effect of decayed teeth on early adolescents’ oral health-related quality of life (OHRQoL). Methods A cross-sectional analytical investigation was conducted on 1020 preparatory schoolchildren selected on the basis of a multistage sampling technique. Caries status of the participants detected via recording their caries experience and untreated cavities using DMFT and DT indices. OHRQoL was determined using a validated Arabic CPQ 11-14 short-form questionnaire. Statistical methods for descriptive analysis, chi-square test, Independent-Samples t test and one-way analysis of variance (ANOVA) were used. Multivariate Poisson regression analysis through a hierarchical approach was used to detect the influence of independent variables on DT scores. To declare the association between independent variables and QoL, a step-by-step, multivariate regression analysis was conducted. Results The average scores of DMFT and DT in this study were 2.97±1.29 and 1.66±1.24. Poisson regression analysis demonstrated that early adolescents whom their mothers with a lower level of education and of low socioeconomic status were 1.41 and 1.27 times respectively had higher DT scores when compared with their peers. Untreated cavities affected mainly by mother education, school type, family income, and regular dental appointments. Children with DMFT≤3) or DT=0 recorded a statistically significant lower CPQ 11-14 average score (p˂0.01) and (p˂0.0001) respectively. Conclusions Untreated carious cavities and caries experience were associated with lower socioeconomic, maternal education andl ess frequent tooth brushing. Untreated carious cavities have a significant negative impact on schoolchildren’s QoL. .
Systematic review of statistical methods for safety data in malaria chemoprevention in pregnancy trials
Authors: Patson Noel , Mukaka Mavuto , Otwombe Kennedy N , Kazembe Lawrence , Mathanga Don P , Mwapasa Victor , Kabaghe Alinune N , Eijkemans Marinus JC , Laufer Miriam K , Chirwa Tobias 
Published: March 2020

Abstract
Background Drug safety assessments in clinical trials present unique analytical challenges. Some of these include adjusting for individual follow-up time, repeated measurements of multiple outcomes and missing data among others. Furthermore, pre-specifying appropriate analysis becomes difficult as some safety endpoints are unexpected. Although existing guidelines such as CONSORT encourage thorough reporting of adverse events (AEs) in clinical trials, they provide limited details for safety data analysis. The limited guidelines may influence suboptimal analysis by failing to account for some analysis challenges above. A typical example where such challenges exist are trials of anti-malarial drugs for malaria prevention during pregnancy. Lack of proper standardized evaluation of the safety of antimalarial drugs has limited the ability to draw conclusions about safety. Therefore, a systematic review was conducted to establish the current practice in statistical analysis for preventive antimalarial drug safety in pregnancy. Methods The search included five databased (PubMed, Embase, Scopus, Malaria in Pregnancy Library and Cochrane Central Register of Controlled Trials) to identify original English articles reporting Phase III randomized controlled trials (RCTs) on anti-malarial drugs for malaria prevention in pregnancy published from January 2010 to July 2019. Results Eighteen trials were included in this review that collected multiple longitudinal safety outcomes including AEs. Statistical analysis and reporting of the safety outcomes in all the trials used descriptive statistics; proportions/counts (n=18, 100%) and mean/median (n=2, 11.1%). Results presentation included tabular (n=16, 88.9%) and text description (n=2, 11.1%). Univariate inferential methods were reported in most trials (n=16, 88.9%); including Chi-square/Fisher`s exact test (n=12, 66.7%), t-test (n=2, 11.1%) and Mann-Whitney/Wilcoxon test (n=1, 5.6%). Multivariable methods, including Poisson and negative binomial were reported in few trials (n=4, 22.2%). Assessment of a potential link between missing efficacy data and safety outcomes was not reported in any of the trials that reported efficacy missing data (n=7, 38.9%). Conclusion The review demonstrated that statistical analysis of safety data in anti-malarial drugs for malarial chemoprevention in pregnancy RCTs is inadequate. The analyses insufficiently account for multiple safety outcomes potential dependence, follow-up time and informative missing data which can compromise anti-malarial drug safety evidence development, based on the available data.
Primary validation of Charm II tests for the detection of antimicrobial residues in a range of aquaculture fish
Authors: Mukota Aziz Kimera , Gondam Melanie Flore Kamini , Tsafack Julie Judith Takadong , Sasanya James , Reybroeck Wim , Ntale Muhammad , Nyanzi Steven Allan , Tebandeke Emmanuel 
Published: March 2020

Abstract
The study carried out a primary validation of Charm II tests for the detection of antimicrobial residues in aquaculture fish. The Validation was performed according to European Commission Decision 2002/657/EC and the parameters determined included: detection capability, repeatability, reproducibility, specificity and robustness for the detection of antimicrobial residues in fish. Fish materials from different species including cat fish, trout, salmon, sea bass, tilapia, lingue and pangasius, were spiked with varying concentrations of selected antibiotics including sulfonamides, beta-lactams, macrolides, tetracyclines and aminoglycosides to determine the detection capabilities and other validation parameters of the Charm II tests. Results of the validation showed that the detection capabilities for the tetracyclines ranged from 25 µg/kg to 100 µg/kg, while the sulfonamides and aminoglycosides were detected at 25 µg/kg for all species under study. The detection capabilities for the beta-lactams ranged from 25 µg/kg to 300 µg/kg; and was 100 µg/kg for the tested macrolides. Results of the study showed that there was no significant difference between counts for samples read immediately after addition of the scintillation fluid and those read fourteen hours after addition of the scintillation fluid, provided that there was good vortexing before analysis. There was also no significant difference between counts for the same samples analyzed in different runs under repeatability and reproducibility conditions at the same spiking concentrations for the different fish species analyzed. The relative standard deviation for both repeatability and reproducibility ranged from 1.2 to 15.1%.The Charm II tests were found to be 100% group specific, as none of antimicrobials kits, gave false positive results when testing non-target antimicrobial drugs. Results of this study prove the specificity and precision of the Charm II assay in the detection of various antimicrobial residuals in fish. The results also demonstrate the suitability of the Charm II technique as a rapid screening tool for detection of antimicrobial residues in a variety of fish species at Maximum Residue Limits established in the EU guidelines, and its applicability for the rapid evaluation of the quality of aquaculture fish for safety and trade purposes.
Antiviral effect of copper chloride on feline calicivirus and Synergy with Ribavirin in vitro
Authors: Li Dengliang , Cui Zhanding , Li Guohua , Zhang Liangting , Zhang Ying , Zhao Han , Zhang Shuang , Guo Yanbing , Zhao Yanli , Men Fanxing , Zhao Shihui , Shao Jiang , Du Dongju , Huang Hailong , Wang Kai , Hu Guixue , Li Tiansong , Zhao Yongkun 
Published: March 2020

Abstract
Background: Feline calicivirus (FCV) is a common pathogen causing widely prevalent upper respiratory disease for kitten and felines in recent years. Due to the substantial genetic variability of the viral genes, existing vaccines cannot provide complete protection. Therefore, researches on FCV antiviral drugs have received much attention. Results: In this study, we found that copper chloride had dose-dependent antiviral effects against FCV in F81 cells. We also found that the combination of copper chloride and ribavirin had a synergistic effect against FCV in the F81 cells. In contrast, the combination of and horse anti-FCV immunoglobulin F(ab’) 2 showed an antagonistic effect, likely because the copper chloride has an effect on the F(ab’) 2 immunoglobulin; however, further research is needed to clarify this supposition. Conclusions: In summary, we found that copper chloride had low cytotoxicity and significant antiviral effects against FCV in F81 cells, providing a new drug candidate for the prevention and treatment of FCV infection.
Using Real-Time Online Preprocessed Mouse Tracking for Lower Storage and Transmission Costs
Authors: Purnama Fajar , Usagawa Tsuyoshi 
Published: March 2020

Abstract
Pageview is the most popular webpage analytic metric in all sectors including blogs, business, e-commerce, education, entertainment, research, social media, and technology. To perform deeper analysis, additional methods are required such as mouse tracking, which can help researchers understand online user behavior on a single webpage. However, the geometrical data generated by mouse tracking are extremely large, and qualify as big data. A single swipe on a webpage from left to right can generate a megabyte (MB) of data. Fortunately, the geometrical data of each x and y point of the mouse trail are not always needed. Sometimes, analysts only need the heat map of a certain area or perhaps just a summary of the number of activities that occurred on a webpage. Therefore, recording all geometrical data is sometimes unnecessary. This work introduces preprocessing during real-time and online mouse tracking sessions. The preprocessing that is introduced converts the geometrical data from each x and y point to a region-of-interest concentration, in other words only heat map areas that the analyzer is interested in. Ultimately, the approach used here is able to greatly reduce the storage and transmission cost of real-time online mouse tracking.
Psychometric properties of the Czech Integrated Palliative Outcome Scale: Reliability and content validity analysis
Authors: Vlckova Karolina , Hoschlova Eva , Chroustova Eva , Loucka Martin 
Published: March 2020

Abstract
Background: Outcome measurement is an essential part of the evaluation of palliative care and the measurements need to be reliable, valid and adapted to the culture in which they are used. The Integrated Palliative Outcome Scale (IPOS) is a widely used tool for assessing personal-level outcomes in palliative care. The aim of this study was to provide Czech version of IPOS and asses its psychometric properties.
Methods: Patients receiving palliative care in hospice or hospitals completed the IPOS. The reliability of Czech IPOS was tested with Cronbach alpha (for internal consistency), the intraclass correlation coefficient for total IPOS score and weighted Kappa (for test-retest reliability of individual items). Factor analysis was used for elucidating the construct (Exploratory Factor Analysis). Convergent validity was tested with correlation analysis (Spearman correlation) in a part of the sample, who completed also the Edmonton Symptom Assessment System (ESAS) and the Palliative Performance Scale (PPS).
Results: The sample consisted of 140 patients (mean age 72; 90 women; 81 % oncological disease). The Cronbach alpha was 0.789; intraclass correlation was 0.88. The correlations of IPOS with ESAS was R= 0.4 and PPS R= -0.2. Exploratory factor analysis revealed a 2-factor solution on our data. The first factor covers emotional and information needs and the second factor covers physical symptoms.
Conclusion: Czech IPOS has very good reliability regarding both internal consistency and test-retest reliability. Together with an item analysis results, we can conclude that the Czech adaptation of the tool was successful. The convergent validity needs to be assessed on the larger sample and the proposed 2-factor internal structure of the questionnaire has to be confirmed by using CFA.
Optimal Partner Wavelength Combination Method Applied to NIR Spectroscopic Analysis of Human Serum Globulin
Authors: Han Yun , Zhong Yun , Zhou Huihui , Kuang Xuesong 
Published: March 2020

Abstract
Human serum globulin (GLB), which contains various antibodies in healthy human serum, is of great significance for clinical trials and disease diagnosis. In this study, the GLB in human serum was rapidly analyzed by near infrared (NIR) spectroscopy without chemical reagents. Optimal partner wavelength combination (OPWC) method was employed for selecting discrete information wavelength. For the OPWC, the redundant wavelengths were removed by repeated projection iteration based on binary linear regression, and the result converged to stable number of wavelengths. By the way, the convergence of algorithm was proved theoretically. Moving window partial least squares (MW-PLS), a well-performed wavelength selection method, was also performed for comparison. The optimal models were obtained by the two methods, and the corresponding root-mean-square error of cross validation and correlation coefficient of prediction (SECV, RP,CV) were 0.813 g·L-1 and 0.978 with OPWC combined with PLS (OPWC-PLS), and 0.804 g L-1 and 0.979 with MW-PLS, respectively. The two methods achieved almost the same good results. However, the OPWC only contained 28 wavelengths, so it had obvious lower model complexity. Thus it can be seen that the OPWC-PLS has great prediction performance for GLB and its algorithm is convergent and rapid. The results provide important technical support for the rapid detection of serum.
Diagnostic performance of individual characteristics and anthropometric measurements in detecting elevated serum alanine aminotransferase among children and adolescents
Authors: Ou Yu-Lan , Lai Yue-Rong , Jiang Chao-Nan , Zhang Jing , Ding Zan 
Published: March 2020

Abstract
Background: Screening for elevated serum alanine aminotransferase (ALAT) can help identifying individuals at the risks of chronic and metabolic diseases, but blood collection is invasive and cannot be widely used for investigations. Considered as simple and inexpensive screening indices, individual characteristics and anthropometric measurements can be measured in a large crowd and may be important surrogate markers for ALAT levels. This study aimed to examine the diagnostic performance of individual characteristics and anthropometric parameters as predictive factors for discerning an elevated ALAT activity among Shenzhen children and adolescents.

Methods: A school-based screening study was performed from 9 high schools in Shenzhen during February 2017 and June 2018. Receiver operating characteristic curve was used to examine the diagnostic performance of each variable for detecting elevated ALAT.

Results: Altogether 7271 students aged 9−17 years were involved. The proportion of elevated ALAT greatly increased with increasing classification of BMI-z. By the sex-specific cut-offs for elevated ALAT (30 U/L boys; 19 U/L girls), BMI showed the highest area under the curve of 0.789 (95% CI 0.765－0.812) and followed by weight (0.779 [0.755－0.802]), BMI-z (0.747 [0.722－0.772]), height (0.622 [0.597－0.647]), and age (0.608 [0.584－0.632]), while height-z was not capable. With the cut-off of 67.8 kg for weight and 22.6 kg/m2 for BMI, the accuracy to identify elevated ALAT was 87.1% for weight and 82.9% for BMI.

Conclusions: The presence of elevated ALAT was more common in overweight or obese children and adolescents. BMI and weight had the superiority of detecting elevated ALAT, followed by BMI-z, height, and age.
Correlation between UGT1A1 gene polymorphism and irinotecan chemotherapy in metastatic colorectal cancer：a study from Guangxi Zhuang
Authors: Chen Shaojun , Hua Li , Feng Chenjun , Mo Qia , Wei Mengzhuan , Shen Yongqi , Lin Zhan , Li Guisheng , Xu Junyi , Guo Chengxian , huang haixin 
Published: March 2020

Abstract
Background: There are obviously ethnic differences between the UGT1A1 gene polymorphisms.Due to the difference of genetic background and environment,the treatment with colorectal cancer patients of Guangxi Zhuang should not completely follow the Euramerican or Chinese han patients.The study aimed to explore the correlation of UGT1A1 gene polymorphism of Guangxi Zhuang metastatic colorectal cancer (mCRC) with irinotecan -based chemotherapy, in order to develop an individualized irinotecan regimen for mCRC patients of Guangxi Zhuang.
Methods: From June 2013 and June 2015, a total of 406 patients of Guangxi who were histologically diagnosed as metastatic colorectal cancer with 86 patients that conformed to inclusion and exclusion criteria were competitively enrolled.The distribution of UGT1A1 gene polymorphism was analyzed-retrospectively in all patients. Pyrosequencing method was used to detect the UGT1A1 *28 and*6 gene polymorphism in the 86 Guangxi Zhuang mCRC patients. After first-line chemotherapy with FOLFIRI regimen, the relationship between gene polymorphism of UGT1A1 and adverse reactions, and efficacy of Irinotecan were analyzed with χ2 test and Kaplan-Meier method.
Results: UGT1A1 *28 wild-type (TA6/6), heterozygous mutant (TA6/7) and homozygous mutant (TA7/7) accounted for 69.8%, 30.2% and 0%, respectively. UGT1A1 *6 wild type (G / G), heterozygous mutation type (G / A) and homozygous mutant (A / A) accounted for 76.7%，20.9% and 2.3%，respectively. UGT1A1 *28 TA6 / 7 type could increase the risk of grade 3~4 diarrhea (p=0.027), which did not increase the risk of grade 3~4 neutropenia (p=0.092). UGT1A1 *6 G / A and A / A type could increase the risk of grade 3~4 diarrhea and neutropenia (p=0.001; p=0.017). After chemotherapy with FOLFIRI, there was no significant difference in response rate (RR) (p=0.729; p=0.745) or in median progression-free survival (mPFS) between the wild-type, mutant treatment of UGT1A1 *28 and UGT1A1 *6 (7.0m vs 7.4m, p=0.427; 6.9m vs 7.0m p=0.408).
Conclusions: The distribution of UGT1A1 *28 and UGT1A1 *6 gene polymorphism in Guangxi Zhuang patients were differed from the existing reported of European people and Chinese Han population. The UGT1A1 gene polymorphism with irinotecan chemotherapy-associated diarrhea and neutropenia were closely related. There was no significant association between UGT1A1 gene polymorphism and therapeutic efficacy of irinotecan.
Occurrence, risk factors and genotypes of Enterocytozoon bieneusi in dogs and cats in Guangzhou, southern China: high genotype diversity and zoonotic concern
Authors: Wang Haiyan , Lin Xuhui , Sun Yongxiang , Qi Nanshan , Lv Minna , Xiao Wenwan , Chen YuanCai , Xiang Ruiping , Sun Mingfei , Zhang Longxian 
Published: March 2020

Abstract
Background: Enterocytozoon bieneusi , a common opportunistic fungal pathogen, has a wide range of hosts. Limited epidemiological data on E. bieneusi intestinal infections in companion animals (dogs and cats) in China exists. In this study, fecal samples (651 from dogs and 389 from cats) in Guangzhou city, Guangdong Province, China, were collected, and the ribosomal internal transcribed spacer region from the DNA extracted from them was PCR-amplified and sequenced. Results: Based on the sequencing data, E. bieneusi was identified in the fecal samples collected from 149 (22.9%) and 79 (20.3%) dogs and cats. Of the factors investigated, poor living conditions appeared be the major risk factor for contracting the pathogen. Eleven E. bieneusi genotypes, six known (PtEb IX, GD1, D,CD9 , EbpC, I) and five novel (designated here as GD2– GD6), were found in dogs. Eight genotypes, six known (PtEb IX, GD1, D, CD9, EbpC, Type IV) and two novel (GD2 and GC1), were identified in cats. Genotype PtEb IX was most common in both dogs and cats, followed by genotype GD1. Conclusions: Although PtEb IX was the most common E. bieneusi genotype in dogs, this is the first report of this genotype dominating in cats. The same genotype distribution of the pathogen between the two different companion animals species in the same geographic area indicates that inter-species transmission is probable. The widespread existence of zoonotic E. bieneusi genotypes (D, EbpC, Type IV) in companion animals indicates that they are potential sources of environmental contamination and infections in humans.