The relationship between children’s accuracy during numerical magnitude comparisons and arithmetic ability has been investigated by many researchers. Contradictory results have been reported from these studies due to the use of many different tasks and indices to determine the accuracy of numerical magnitude comparisons. In the light of this inconsistency among measurement techniques, the present study aimed to investigate this relationship among Iranian second grade children (n = 113) using a pre-established test (known as the Numeracy Screener) to measure numerical magnitude comparison accuracy. The results revealed that both the symbolic and non-symbolic items of the Numeracy Screener significantly correlated with arithmetic ability. However, after controlling for the effect of working memory, processing speed, and long-term memory, only performance on symbolic items accounted for the unique variances in children’s arithmetic ability. Furthermore, while working memory uniquely contributed to arithmetic ability in one-and two-digit arithmetic problem solving, processing speed uniquely explained only the variance in single-digit arithmetic skills and long-term memory did not contribute to any significant additional variance for one-digit or two-digit arithmetic problem solving. Attaining arithmetic ability is a main academic skill children learn during elementary school years. It provides the foundation for learning higher forms of mathematics such as fraction, ratio, proportion, percentages and algebra. Successes in daily life, society, and labor increasingly depend on this quantitative skill. Difficulties in performing arithmetic skills may face children with substantial problems in educational setting and negatively interfere with their daily experiences throughout life. In order to provide scientifically appropriate remedial teaching strategies for children suffering from mathematical difficulties, a number of researchers tried to find both specific numerical and general cognitive factors underlying arithmetic ability e.g., . HoweverWe aimed to measure performance on symbolic and non-symbolic numerical magnitude comparisons using the Numeracy Screener, working memory, processing speed, and long-term memory and determine their contribution to arithmetic ability among second-grade Iranian children. The main research question is whether variability in children’s scores on symbolic or non-symbolic items of the Numeracy Screener could uniquely explain the variability in single-digit or two-digit arithmetic problem solving after controlling for the effect of working memory, processing speed, and long-term memory, as these are domain-general cognitive skills related to mathematical abilities. Before detailing the specifics of the method used, the literature describing numerical magnitude comparison and its contribution to children’s arithmetic ability will be reviewed. In addition, the roles of working memory, processing speed, and long-term memory as three domain-general cognitive abilities influencing children’s arithmetic development will be briefly explained.In recent years, psychologists have proposed that humans and many other species have an inherent sense of quantity known as “Approximate Number Sense” (ANS). This mental number representation system allows approximate estimation of quantities without counting. When observing different non-symbolic magnitudes , our ANS enables us to implicitly discriminate between smaller and larger ones . Our accuracy performing these non-symbolic comparisons dramatically changes from infancy to adulthood. . This imAfter going to school, children acquire a new symbolic system for representation of magnitudes. Similar to the pre-existing non-symbolic system, the new system allows children to manipulate or compare magnitudes, but in symbolic forms such as words that represent numbers or Arabic digits. To compare quantities using symbolic representations , researchers assumed that children need to map the acquired symbolic system onto an already-existing non-symbolic system . In otheDuring recent decades, it has been assumed that numerical magnitude processing is related to arithmetic development in children. In building a body of behavioral and theoretical evidence related to numerical magnitude processing in early life and its correlation with arithmetic ability in children, several researchers have used different numeracy comparison computerized tasks to explore the relationship between both symbolic and non-symbolic numerical magnitude comparison and previous, concurrent, or future arithmetic ability in children. However, these researchers reported contrasting results see , other hA possible explanation of the contrasting results reporting the relationship between numerical knowledge and arithmetic ability is that no commonly accepted, identical version of the magnitude comparison task exists . To asseAn identical test intended to use just the accuracy index to measure the acuity during the comparison of magnitudes is the “Numeracy Screener” . In thisAfter demonstrating the validity of the Numeracy Screener by finding age-related improvements in the accuracy of numerical comparisons, the researchers  tried toIn addition to numerical magnitude comparison processing as a domain-specific numerical ability, other domain-general cognitive factors might explain individual differences in children’s arithmetic abilities. Working memory, processing speed, and long-term memory are three cognitive abilities that may have a significant impact on individual differences in the arithmetic abilities of different children . Before In the process of solving single-digit arithmetic problems, children pass through simpler to more advanced strategies. First, they learn to use a procedure in which they count all of the numbers, a procedure of obtaining a sum in which both addends are counted to find the solution. Then, they learn to use “counting on” (or min) procedures, in which they state the value of the larger addend before counting the smaller one. In both strategies, children may use their fingers for counting or count aloud. Finally, frequent use of counting strategies leads to the formation of long-term memory association between problems and their answers, eventually resulting in direct retrieval of answers from long-term memory when solving simple arithmetic problems . As mentWorking memory generally refers to a limited-capacity information-processing resource engaged in two key processes, the storage of information and the simultaneous processing of the same or other information . It is aProcessing speed refers to the cognitive ability to execute simple cognitive tasks rapidly and efficiently  magnitude comparisons uniquely explain the variability in arithmetic scores in the presence of working memory, processing speed, and long-term memory.N = 113) from four different classrooms. Using Raven’s Standard Progressive Test  tasks were administered to measure each subject’s arithmetic ability. The two tests were a single-digit arithmetic problem solving test (labeled the “Math Fluency” test) and a two-digit arithmetic problem solving task . The math fluency test assessed the participant’s ability to quickly solve single-digit arithmetic problems. During the task, children were asked to solve 20 simple addition problems  and 20 simple subtraction problems ; one minute was given for each section, during which children were to complete as many problems as possible. Half of the participants started with addition, half with subtraction. The number of correct answers for each task represented the score on that one.The calculation task assessed the ability of participants to solve addition and subtraction problems involving two-digit numbers. Students were required to complete 10 problems in which they added two two-digit numbers  and then to solve 10 similar subtraction problems . The order in which the tasks were presented was similar to the order for the math fluency tasks.Since two-digit arithmetic tasks may require more abstract reasoning, further attentional resources, and basic arithmetic skills, any time pressure may negatively affect child’s performance accuracy. Thus, unlike the math fluency problems, there was no time limitation in these tasks. The score on the tests was the number of correct answers for each task.“Counting Span” is a well-known task to measure working-memory capacity. This task was originally presented by The “WJ-III Visual Matching Task” (WJ is for “Woodcock-Johnson”) was used to measure processing speed . In thisTo measure semantic long-term memory, we used Retrieval Fluency, described in The means and standard deviations  of all variables were presented in As is shown in Based on Since comparisons of both symbolic and non-symbolic magnitudes were moderately related to all arithmetic skills, in order to get more information about the unique contribution of each magnitude comparison to both math fluency and calculation skills, four linear regression analyses were conducted, two for single-digit addition and subtraction and two for two-digit addition and subtraction. The major focus of these analyses was to carefully examine the independence of each numerical magnitude comparison to predict single-digit and two digits addition and subtraction skills while controlling for the effect of working memory, processing speed, and long-term memory. For this purpose, all of the variables were entered in one step. The results were presented in F  = 9.563, p < .001, 2R = .31). In this model, performance on working memory, processing speed, and symbolic comparison explained the significant and unique variance in single digit addition. Conversely, non-symbolic magnitude comparison and long-term memory did not uniquely explain the variance in that. The second linear regression analysis, which used single-digit subtraction as a dependent variable, was also significant  = 6.211, p < .001, R2 = .23). In this model, similar to first model, symbolic comparison, working memory, and processing speed had significant and unique contributions to single-digit subtraction. However, non-symbolic comparison and long-term memory did not account for significant and unique contributions to (or variances in) single-digit subtraction skill.F  = 5.322, p < .001, 2R = .22). In this model, performance on working memory, and symbolic comparison explained the significant and unique variance in two- digit addition. Conversely, non-symbolic magnitude comparison, processing speed, and long-term memory did not uniquely explain the variance in that. The forth linear regression analysis, which used two-digit subtraction as a dependent variable, was also significant  = 6.321, p < .001, 2R = .24). In this model, similar to third model, symbolic comparison and working memory had significant and unique contributions two-digit subtraction. However, non-symbolic comparison, processing speed, and long-term memory did not account for significant and unique contributions to (or variances in) two-digit subtraction skill.The present study explored whether performance on the symbolic and non-symbolic items of a Numeracy Screener is related to individual differences in the arithmetic ability of second grade children in Iran. The arithmetic skills measured included single-digit addition and subtraction tasks and series of two-digit addition and subtraction problems. Furthermore, we intended to determine whether magnitude comparison tasks significantly explain variances of single-digit and two-digit addition and subtraction skills over some general cognitive factors including working memory, processing speed, and long-term memory.We found that participants’ scores on both symbolic and non-symbolic items were significantly correlated with scores on single-digit and two-digit arithmetic. Participants who scored highly on symbolic or non-symbolic magnitude comparison tasks on the Numeracy Screener also tended to receive high scores on single-digit and two-digit arithmetic. Nevertheless, the results of our regression analyses demonstrated that only participants’ scores on the symbolic items of the Numeracy Screener uniquely explain the variances in both single-digit and two-digit addition and subtraction skills. These findings are closely comparable with the results reported by Our data also support the commonly held assumption that symbolic magnitudes are acquired through a process in which the mapping symbolic system is mapped onto a previously existing non-symbolic system . The sigThe results of our regression analyses also revealed that working memory uniquely explains the variance in both single-digit and two-digit arithmetic, in the presence of the unique contribution of symbolic magnitude comparison. The central role of working memory in developing children’s arithmetic ability have been reported by several studies e.g., . It has To elaborate further, the regression analyses revealed that processing speed uniquely contributed to single-digit and two-digit addition and subtraction, but not to two-digit arithmetic. It has been assumed that, in solving arithmetic problems, processing speed may facilitate counting speed to successfully pair problems and their answers in available working memory capacity before decay begins. More efficient and faster pairing of problems and their answers in limited working memory capacity result in more established long-term memory representations . Bull anIn line with In conclusion, the current findings demonstrated that significant relationships exist between the performances of second-grade primary school children in Iran on the Numeracy Screener items as well as on both measured arithmetic abilities (single-digit and two-digit arithmetic). In addition, it was found that only the symbolic comparison portion of the Numeracy Screener accounted for unique variances in both single-digit and two-digit arithmetic. These results are in line with previous research in which the Numeracy Screener was initially used  and highThe current findings demonstrated that a combination of numerical magnitude comparison tasks assessed via a Numeracy Screener, memory, and processing speed explain 30% and 22% of the variances in math fluency and calculation skill, respectively. The remaining variances might be explained by other domain-specific factors such as number line estimation, subitizing ability, counting knowledge, or other domain-general cognitive abilities such as attentive behavior, inhibition, task switching, language, and intelligence. Further research is recommended to determine the relationship between the Numeracy Screener, the other factors summed up above, and arithmetic ability in primary school children, especially in other developing countries.


Anti-glycyl-tRNA synthetase (anti-EJ) antibody is occasionally positive in patients with interstitial lung disease (ILD). We aimed to define the clinical, radiological and pathological features of patients with anti-EJ antibody-positive ILD (EJ-ILD).We retrospectively analyzed the medical records of 12 consecutive patients with EJ-ILD who underwent surgical lung biopsy.The median follow-up time was 74 months . The median age was 62 years . Seven of 12 patients were female. Eight patients presented with acute onset. Six patients eventually developed polymyositis/dermatomyositis. On high-resolution computed tomography, consolidation and volume loss were predominantly observed in the middle or lower lung zone. Nine patients presented pathologically nonspecific interstitial pneumonia with organizing pneumonia, alveolar epithelial injury and prominent interstitial cellular infiltrations whereas the other three patients were diagnosed with unclassifiable interstitial pneumonia. Although all patients but one improved with the initial immunosuppressive therapy, five patients relapsed. When ILD relapsed, four of the five patients were treated with corticosteroid monotherapy. Four of the six patients without relapse have been continuously treated with combination therapy of corticosteroid and immunosuppressant.Patients with EJ-ILD often had acute onset of ILD with lower lung-predominant shadows and pathologically nonspecific interstitial pneumonia or unclassifiable interstitial pneumonia with acute inflammatory findings. Although the disease responded well to the initial treatment, relapse was frequent. Because of the diversity of the clinical courses, combination therapy of corticosteroid and immunosuppressant should be on the list of options to prevent relapse of EJ-ILD. Interstitial lung disease (ILD) is caused by various etiologies including collagen vascular disease, drug induced and inhalation exposure. Patients with ILD often have collagen vascular disease-related autoantibodies even when they do not fulfill the diagnostic criteria for any collagen vascular diseases . In 2015Anti-ARS antibodies are positive in 20%–35% of patients with polymyositis/dermatomyositis (PM/DM) . AlthougOn computed tomography (CT), patients with ARS-ILD often have radiologically traction bronchiectasis, consolidation and volume loss predominantly in the lower lung zones , 11, 12.However, there are only a few reports describing the clinical features of patients with ILD with positive-anti-EJ antibody (EJ-ILD) , 16. TheWe retrospectively analyzed the medical records of 12 consecutive patients with EJ-ILD who underwent surgical lung biopsy at Kanagawa Cardiovascular and Respiratory Center between March 2005 and April 2013 and were subsequently followed up for over one year. Anti-ARS antibodies were detected with an immunoprecipitation assay at Tokai University School of Medicine as previously described method .We obtained the clinical presentations, physical findings, laboratory findings and pulmonary function tests at the initial visit from patients’ medical records. The diagnosis of PM/DM was based on Bohan and Peter’s criteria . PatientCT images before biopsy were obtained from all the 12 patients. All images were reviewed independently by two experienced radiologists without any prior knowledge of the clinical and pathological information.To determine the distribution and extent of parenchymal abnormalities, each lung was divided into three zones of upper, middle and lower at the level of the carina and the left inferior pulmonary vein. The following high resolution CT (HRCT) findings were coded as present or absent in each zone: reticulation, ground-glass opacity, consolidation, bronchovascular thickening, traction bronchiectasis, honeycombing, volume loss and emphysema. Radiological assessment was based on those from previous studies , 20. DisBiopsy was performed in all patients. Multiple specimens mainly from the upper and lower lobes were obtained from 11 of 12 patients. All the specimens were stained with hematoxylin-eosin and Elastica van Gieson and were reviewed independently by two experienced lung pathologists who were not aware of the clinical and radiological findings. Pathological patterns were diagnosed according to the 2002 and 2013 ATS/ERS consensus classification of the idiopathic interstitial pneumonias and 2008 ATS project for idiopathic NSIP , 22.The intensity and extent of the following pathological features were semi-quantitatively graded as absent, mild, moderate or severe: pleural fibrosis, pleuritis, lymphoid follicles with germinal center, organizing pneumonia, alveolar epithelial injury, interstitial cellular infiltration, alveolar wall fibrosis, microscopic honeycombing, fibroblastic focus and collapse. Pathological assessment was based on those from previous studies , 23, 24.Disagreements between the two pathologists were discussed until consensus was reached.The clinical course and treatment response of EJ-ILD was evaluated on the basis of the degree of changes in both chest images and pulmonary functions. Two radiologists evaluated the chest radiograph and/or HRCT. We graded the changes in pulmonary functions according to the 2000 ATS/ERS consensus statement for idiopathic pulmonary fibrosis Table  25]. In. In25]. The initial response was assessed within six months after the initiation of treatment. After the initial evaluation, we assessed all chest radiographs and pulmonary functions until the end of the follow-up period. The relapse of ILD meant that the patients with deterioration needed to reinforced therapy for ILD.The summary of the clinical characteristics of the 12 patients is listed in Table At the disease onset, extra-pulmonary symptoms were observed in only five patients, whereas all patients presented pulmonary symptoms. Only one patient was suffering from muscle weakness. Among six patients diagnosed with IPAF and anti-synthetase syndrome, no patient had skin involvement, and only one patient presented articular symptoms. Two patients have not had extra-pulmonary symptoms during entire follow-up period Table . Palmar Creatine kinase levels were elevated in three patients and lactate dehydrogenase levels were elevated in eight, while all patients presented with the elevation of erythrocyte sedimentation rate, C-reactive protein, Klebs von den Lungen-6 and surfactant protein-D levels. Electromyography, muscle biopsy and magnetic resonance imagings of muscle were performed in only two DM patients.Specific autoantibodies other than anti-EJ antibody were found in only one patient who had anti-SSA antibody at the initial visit and was diagnosed with Sjögren’s syndrome 20 months after the diagnosis of EJ-ILD. Other patients had neither other autoantibodies nor the diagnosis of any other collagen vascular diseases except for PM/DM.Six patients were diagnosed with PM/DM during the disease course and five of them were of the ILD-preceding type. Others were all diagnosed with idiopathic interstitial pneumonia and satisfied with the proposed criteria of both IPAF and anti-synthetase syndrome.The HRCT findings are described in Table The median interval between the date of HRCT and biopsy was 28 days . Four patients were pathologically diagnosed with cellular NSIP (c-NSIP), five were with fibrosing NSIP (f-NSIP), and three were with unclassifiable interstitial pneumonia. Organizing pneumonia, alveolar epithelial injury, interstitial cellular infiltration, pleural fibrosis and collapse with moderate or severe grade were observed in more than half of the patients  increased immediately after the initial treatment and remained almost stable between the initial evaluation period . ILD relapsed in five of the 11 improved patients after a median of 46 months  from treatment initiation. Among the five relapsed patients, four were on prednisone monotherapy and four presented with acute onset of the disease. There were few differences in the changes on chest radiograph and pulmonary function test between the relapsed patients and non-relapsed patients until relapse. However, upon relapse, the loss of lung volume was clearly recognized in chest radiograph, and both %FVC and %DLWe retrospectively evaluated the clinical, radiological, pathological features and long-term clinical courses of 12 patients with EJ-ILD who underwent surgical lung biopsy. We have shown that patients with EJ-ILD had often acute onset of ILD with lower-lung predominant shadows with volume loss on HRCT, pathologically NSIP or unclassifiable interstitial pneumonia with acute inflammatory findings, and good response for initial steroid therapy, although relapse was frequent among the patients with corticosteroid monotherapy. In most patients with EJ-ILD clinical disease behavior was reversible or progressive and irreversible disease. Although anti-EJ antibodies correlated well with ILD, there are a few reports which describe the clinical, radiological and pathological findings of EJ-ILD and no reports describe any detailed clinical courses , 26. To The onset of EJ-ILD was often acute in the present study. EJ-ILD progressed within three months in previous literature , 16. FifFifty percent of patients in this cohort were ultimately diagnosed with PM/DM, which was consistent with the previous report , 10. HowRegarding to IPAF and anti-synthetase syndrome, almost no patient presented physical symptoms at initial visit. However, a half of them developed muscular symptoms and fever during follow-up period. This result is also compatible with the previous report . These sThe HRCT findings were basically compatible with those of previous reports on ARS-ILD and ILD associated with PM/DM , 20, 30.Pathologically unclassifiable interstitial pneumonia and NSIP were observed in our study although recent reports showed that the histopathological patterns of ARS-ILD were NSIP, UIP, ALI and DAD , 15, 16.In this study, the initial treatment response of EJ-ILD and the rate of relapse were similar to those previously reported for ARS-ILD . AlthougThis study has several limitations. First, it was a retrospective study with a small sample size. Second, since this study was performed in a specialized single-center for the respiratory diseases, there might be a selection bias for the diagnosis of PM/DM at the initial visit. However, in fact, all patients except patient #12 had muscle weakness at the initial visit.We delineated the long-term clinical characteristics of EJ-ILD. Because of the diversity of the clinical course, combination therapy of corticosteroid and immunosuppressant should be argued on a case-by-case basis to prevent relapse of EJ-ILD. We need to conduct long-term observation to assess clinical behavior and prevent complications of EJ-ILD.


The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power.Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB ( According to the central dogma, all proteins are synthesized via translation process. Therefore, translation is a key regulatory step for all living organisms, linking transcriptome and proteome . PreviouTwo major methods of translatome investigations are RNC-seq (sequencing of ribosome-nascent-chain attached mRNA)  and RiboHowever, both RNC-seq and Ribo-seq experiments are tricky and cost intensive , thus raising request on a comprehensive database to collect up-to-date translatome sequencing data for various species and conditions, and also a unified, convenient, accurate and robust analysis pipeline to integrate previous data and user-generated data.So far, no previous database includes RNC-seq data, and only a few databases were specifically designed for Ribo-seq. Certainly, these Ribo-seq databases provide valuable online browser, e.g. hosting the RFP and corresponding mRNA data sets in dozens of studies . Except http://www.translatomedb.net). Thanks to the recent Ribo-seq and RNC-seq developments, we have opportunity to collect 10 RNC-seq, 2453 Ribo-seq and their 1394 corresponding mRNA-seq datasets in the published translatome sequencing datasets for 13 major species including human, mouse, rat, zebrafish and yeast, etc. All datasets can be browsed and searched according to their metadata. Considering the high heterogeneity of the experimental procedures and data quality of these datasets, a unified, accurate and robust analysis pipeline is needed to minimize the bias. Therefore, we used FANSe3 algorithm  and Short Read Archive (SRA) databases. The current version includes 2453 Ribo-seq, 1397 mRNA-seq and 10 RNC-seq data sets in 13 species: Arabidopsis, Bacillus, Caenorhabitis, Drosophila, –split-files. The barcode or index part of each read were trimmed.SRA files were fetched from NCBI SRA database and converted to FASTQ format by SRAToolkit v2.8.2 with the parameter mRNA-seq, RNC-seq and Ribo-seq reads were mapped using FANSe3 against transcriptome reference sequences . When maP-value. Translational efficiency (TE), TR and EVI were calculated using the multiple types of sequencing on one sample  of the dataset including the hyperlink to the corresponding articles and a direct FTP download link of the raw sequencing dataset. Alternatively, users may also browse datasets by clicking on the species list on the left side of the homepage, or type in key words into the ‘quick search’ box on the top of the homepage. Search results can be further refined by typing in more keywords in the other fields. In the ‘Details info’ page of each dataset, the gene quantification list, including read count, rpkM and detailed gene information, is provided, which can be browsed and searched.2 fold change (logFC) and P-values represented by this dot  are listed as text tables. All columns can be sorted and all fields can be searched, for example, typing in the gene name in the ‘Search’ box will quickly locate the desired gene and its corresponding values. The table can be downloaded as six common formats, including plain text table, csv, xml and Microsoft Excel format, for further analysis or plotting. Clicking ‘DEGs’ button triggers an interactive table that can filter the DEGs based on user-defined P-value. This facilitates users to export the DEG list for further gene ontology and pathway analyses . Therefore, the regulation in transcriptional level and translational level can be quantitatively evaluated, respectively. Select two datasets and click ‘Compare’ button to compare the metadata for the user to confirm that these two datasets are of his/her interest. For the user's convenience, the same attributes of both datasets were merged and marked as grey and may be also hidden. Then, clicking the ‘Differential Expression Analysis’ will perform the DGE analysis using edgeR software package due to its superior performance on minimized false positives and false negatives . The calt Figure . A detais Figure .Data Comparison section, the list can be searched and downloaded in six formats.This section performs the calculation of the translation indices TE, TR and EVI, which quantitatively represents the translational initiation efficiency and elongation velocity. TE is calculated by the Ribo-seq data and the corresponding mRNA data to contribute the dynamic range of gene expression; TR can be calculated using the mRNA-seq and the corresponding RNC-seq data to reflect cellular functions and phenotypes; EVI can be calculated using the mRNA-seq, the corresponding RNC-seq and Ribo-seq data to reflect protein co-translational folding efficiency. Since TE, TR and EVI are calculated based on rpkM values of each gene in different sequencing types, the corresponding rpkM values are also listed Figure . Similarhttps://www.ncbi.nlm.nih.gov/sra) and get the publicly available SRA FTP URL, then click Submit page of TranslatomeDB, register or log in into the user account, fill in the required information including SRA FTP URL. After submitting all these information, the TranslatomeDB will automatically fetch the data from SRA and start processing the data using the unified pipeline . The computational intensive mapping and quantification process is solely done in the Chi-Cloud, the supercomputer-based cloud NGS analysis system developed and operated by Chi-Biotech Co. Ltd. Therefore, the users simply need just one-click without any powerful workstations or bioinformatics knowledge for all these analysis process. Users may log into their account to check the progress of data processing, as the data fetch and mapping takes some time. The results will be stored in the TranslatomeDB under the user’s account and thus can be searched and analyzed in all other sections. In the ‘My Data’ page, users can manage their datasets.Users can submit their own translatome sequencing datasets  for analysis. To do so, users need to submit their FASTQ datasets to NCBI SRA  more comprehensive collection including RNC-seq, Ribo-seq and mRNA-seq datasets; (ii) much more datasets collected; (iii) offers DGE analysis to compare two datasets, even from two studies; (iv) calculates TR and EVI to quantitatively assess the translation initiation efficiency and elongation speed; (v) one-click, cloud-based analysis of user-uploaded datasets without local computational resources or bioinformatics skills. TranslaomeDB is designed mainly to quantitatively evaluate the global translation. Therefore, it does not pile up RPF reads to predict individual translation initiation and termination sites. For these purposes, RPFdb  and GWIPTo keep the database up-to-date, we will be updating the content in two ways: (i) we will repeat literature search and supplement the newest translatome-related datasets one to two times per year or more frequently; (ii) we will integrate the user-uploaded and analyzed datasets into our main database.R > 0.999). An example of the dataset SRR1257177 can be found in Since a major function of TranslatomeDB is the processing of large and raw sequencing datasets, which is very computationally intensive, the computational cost partly determines the long-term sustainability. Previous tests showed that FANSe2 (for links, see We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power.Supplementary DataClick here for additional data file.


Increased arterial stiffness is an important determinant of the risk of cardiovascular disease. Lipid profile impairment, especially hypercholesterolemia, is associated with stiffer blood vessels. Thus, the aim of this study was to determine which of the five circulating lipid components (high-density lipoprotein cholesterol (HDL-C), non-high-density lipoprotein cholesterol (non-HDL-C), low-density lipoprotein cholesterol (LDL), total cholesterol (TC) and triglycerides) is the best predictor of increased arterial stiffness in an urban Brazilian population.A random sample of 1,662 individuals from the general population of Vitoria, Brazil (25-64 years), was selected, and lipid components were measured using standard methods. Pulse wave velocity was measured using a non-invasive automatic device, and increased arterial stiffness was defined as a pulse wave velocity ≥10 m/s.p=0.04) was associated with the risk of increased arterial stiffness. In women, HDL-C  and non-HDL-C  were good predictors of the risk of increased arterial stiffness. However, these associations were only found in postmenopausal women .In men, only total cholesterol (OR=1.59; CI=1.02 to 2.48, Our findings indicate that both HDL-C and non-HDL-C are good predictors of the risk of increased arterial stiffness in postmenopausal women in an urban Brazilian population and may be useful tools for assessing the risk of arterial stiffness. Increased arterial stiffness is an important determinant of cardiovascular disease (CVD) risk Changes in the lipid profile, especially hypercholesterolemia, may contribute to changes in vascular stiffness Based on this scenario and on the clinical applicability of lipid profile and arterial stiffness measurements, the aim of this study was to determine which of the five measurements recommended to assess cardiovascular risk  and triglycerides) is the best predictor of the risk of increased arterial stiffness in an urban Brazilian population. Moreover, we also assessed the possible influence of menopause on PWV values.A study of the risk factors for CVDs was performed in the urban population of Vitoria, Brazil, using the WHO-MONICA Project guidelines 2).Anthropometric parameters were measured according to a standard protocol Blood glucose levels, triglyceride levels and lipoprotein fractions were assayed with standard techniques using 12-h fasting blood samples Carotid-femoral PWV was measured with the patient in the supine position with an automatic and validated device  operated by an experienced observer who was blinded to the patients’ clinical characteristics. Briefly, common carotid artery and femoral artery pressure waveforms were recorded non-invasively using pulse-sensitive transducers. PWV was measured within a period ranging from 10–15 seconds, and carotid-femoral distance was used to assess PWV. The distance between the recording sites (D) was measured, and PWV was calculated automatically as PWV=D/t, where (t) is the pulse transit time. The measurements were repeated over 10 different cardiac cycles. According to recent recommendations, increased arterial stiffness was defined as a PWV≥10 m/s Information regarding the menopausal statuses of the women in the present study was evaluated using a questionnaire that was completed by each participant in an interview during the clinic visit. The questionnaire was based on the WHO-MONICA epidemiological instrument Categorical variables are presented as percentages, whereas continuous variables are presented as the mean±standard deviation. Binary logistic regression analysis was performed to evaluate the associations between lipid profile parameters  and arterial stiffness, allowing for covariates (mean blood pressure and age). The data are presented as odds ratios (ORs) and 95% confidence intervals (CIs). The same analysis was also performed second time only for women and was stratified by menopausal status . Statistical analyses were conducted using IBM SPSS Statistics for Windows, Version 19.0. Armonk, NY, USA, with the level of significance set at 5%.The results are presented such that they emphasize the relationship between lipid components and increased arterial stiffness in women because some lipid components were strongly associated with increased arterial stiffness in this group, especially in postmenopausal women.Stratified by sex, the demographic data related to age, BMI, waist circumference, fasting glucose, PWV, TC, HDL-C, LDL-C, non-HDL-C, very-low-density lipoprotein cholesterol (VLDL), triglycerides and the presences of diabetes, smoking, hypertension, hyperlipidemia and increased arterial stiffness for the entire sample are summarized in p=0.04) was significantly associated with increased arterial stiffness (p=0.01) and non-HDL-C  were known to be good predictors of the risk of increased arterial stiffness   . AccordiThe main finding of our study was that there were positive associations between HDL-C and non-HDL-C and increased arterial stiffness in postmenopausal women. These results were not replicated in men and premenopausal women. In addition, postmenopausal women displayed higher LDL-C, triglyceride, TC, non-HDL-C and PWV levels than premenopausal women.In the last few decades, researchers have noted an association between aging and dyslipidemia. In men, lipid profiles become more unfavorable because of the decreases in testosterone levels that occur with age. Similarly, in women, menopause is associated with a more atherogenic lipid profile than premenopausal status Increased central arterial stiffness is an important determinant of CVD risk Several studies have focused on the relationship between the lipid profile and arterial stiffness. Holewijn et al. In the present study, non-HDL-C was a good predictor of the risk of increased arterial stiffness in postmenopausal women belonging to an urban Brazilian population. Our data were partially corroborated by the results of several population studies demonstrating that non-HDL-C is a better marker of CVD risk than LDL-C alone Our study had some limitations. First, we did not obtain measurements of follicle stimulating hormone (FSH) levels; therefore, we were unable to make a laboratory diagnosis of menopause. Second, this study was a cross-sectional analysis. Therefore, a causal relationship between increased arterial stiffness and poor lipid profiles could not be established. Third, in our study, some women were treated with postmenopausal hormone replacement therapy. Fourth, hypolipidemic therapy can decrease arterial stiffness In summary, this study showed that non-HDL-C may be a good predictor of the risk of increased arterial stiffness in postmenopausal women. Thus, we surmise that non-HDL-C may a useful tool for the assessing the risk of arterial stiffness during the postmenopausal period.Alvim RO, Magalhães GL and Mourao-Junior CA participated in the design of the study, performed the statistical analysis and drafted the manuscript. De Oliveira CM and Mill JG contributed to the acquisition and interpretation of the data. Krieger JE contributed to the conception and design of the study. Pereira AC conceived the study, participated in its design, and coordinated and assisted with the drafting of the manuscript. All authors read and approved the manuscript.


Growing evidence from recent studies has revealed that microRNA-203 (miR-203) might be an attractive prognostic biomarker for cancer. But controversy still remains. The aim of this meta-analysis was to summarize available evidences and clarify the preliminary predictive value of miR-203 for prognosis in cancer patients. Eligible studies were identified through multiple research strategies in PubMed, EMBASE and Web of Science up to October 2015. Key statistics such as pooled hazard ratios (HR) with 95 % confidence intervals (CIs) were utilized to calculate patient survival. 13 eligible studies with 1600 patients were ultimately enrolled in this meta-analysis. Our results failed to show a significant relation between upregulated miR-203 expression and a favorable overall survival (OS)  in a random effect model. However, in subgroup analysis, we found that high expression of miR-203 was significantly associated with poor OS in Caucasian patients . In contrast, for Asian patients, over-expression of miR-203 was an independent prognostic factor for better and OS . It also suggested that cancer types and miRNA assay method were significant associated with prognosis. The over-expression of miR-203 was effectively predictive of worse prognosis in breast cancer , pancreatic cancer , ependymoma , but for glioma patients, elevated miR-203 is a potential biomarker for predicting better progression of cancer . Besides, for direct miRNA profiling studies, over-expression of miR-203 was an independent prognostic factor for worse OS . This meta-analysis indicated that ethnicity, tumor type and miRNA assay method mainly contributed to heterogeneity. Considering the insufficient evidence, further relevant studies are warranted. MicroRNAs (miRNAs) represent a class of non-coding, highly conserved single stranded RNAs of approximately 22 nucleotides  , EMBASE (http://store.elsevier.com/embase) and Web of Science (www.isiknowledge.com), to identify relevant studies published before 6 October 2013. The search strategy included the following combinations of the keywords: ‘microRNA 203’, ‘cancer OR carcinoma OR tumor OR malignancy’ and ‘prognosis OR survival OR mortality OR death OR relapse OR recurrence OR outcome’. The titles, abstracts, full texts and reference lists of retrieved articles were carefully scanned to identify additional eligible studies.We systematically searched online databases, including PubMed (Eligible studies had to meet the following criteria: (1) English publications; (2) a focus on patients with any type of carcinoma; (3) the association between miR-203 expression and survival outcome. Other exclusion criteria included studies were: (1) review articles or letters; (2) duplicate publications; (3) lacked sufficient data.For each included study, the following data elements was collected: trial features ; characteristics of the participants ; detection method; follow-up time and data needed for prognosis meta-analysis . An HR of >1 was considered significant association with increasing risk of mortality or recurrence. If only Kaplan–Meier curves were reported, the data were extracted from graphical survival plots and HR was estimated using previously described methods  were conducted as Tierney’s method , the random effect model was applied to calculate the pooled HR and its 95 % CI. Figure The data of 1600 patients with multiple cancers from USA, China, Germany, Japan, Denmark among the included studies was summarized for overall survival (OS) analysis. Since significant heterogeneity among the studies was observed , but for the Caucasians, miR-203 high expression was demonstrated to moderately predict poor OS  . In order to explore potential sources of heterogeneity, subgroup analyses were performed according to ethnicity, cancer types and miRNA assay method. The subgroup analysis results suggested that high expression of miR-203 was significantly associated with poor OS of cancer patients among Caucasians people , but in Asians, a better OS associated with elevated miR-203 expression . Based on the analysis results, ethnicity seems to play a crucial role in association of miR-203 expression and cancer patient prognosis, which mainly due to the variations in genetic background, environmental factors. It was also summarized that cancer types have a considerable impact on the prognostic role of miR-203. High expression of miR-203 moderately predicted poor OS in breast cancer, pancreatic cancer and ependymoma patients, but for glioma patients, high miR-203 expression was significantly associated with better OS. Besides, over-expression of miR-203 was an independent prognostic factor for worse OS when direct miRNA profiling assay method was used. Generally speaking, our results show that miR-203 may not be sufficient to predict cancer prognosis and the ethnicity, cancer types and miRNA assay method may be the main source of discrepancies.Nonetheless several limitations exist in the present meta-analysis study. First, more and more attention are focused on prognostic role of miR-203 in cancer, but the studies we included are all from Asians and Caucasians, the cancer styles are not comprehensive too; hence, further studies explored the prognostic value of miR-203 on various ethnicities and cancer styles may be needed. Secondly, the numerical value of pooled HR was not sufficiently strong to indicate the prognosis although we have demonstrated the correlation of high miR-203 expression with the overall survival in Caucasians and Asians. Thirdly, we extracted the data form survival curves if the studies didn’t provide HR, which might be of less credibility compared with direct analysis on HR. Despite of the limitations, our study is the first meta-analysis to evaluate the prognostic role of miR-203 in cancer.In summary, our findings showed that miR-203 may not be sufficiently accurate as a prognosis for human cancer. But we explored that elevated miR-203 expression might potentially predict the poor survival in Caucasian people while was significantly correlated with good overall survivals in Asians. Besides, tumor type and miRNA assay method may be the potential sources of heterogeneity. More clinical investigations with larger sample size should be conducted to focus on the relationship between miR-203 expression and patient prognosis.


Salivary T  measurement by liquid chromatography–tandem mass spectroscopy resents the opportunity to examine health correlates of Sal-T in a large-scale population survey.This study sought to examine associations between Sal-T and health-related factors in men and women age 18–74 years.Morning saliva samples were obtained from participants in a cross-sectional probability-sample survey of the general British population . Self-reported health and lifestyle questions were administered as part of a wider sexual health interview.Study participants included 1599 men and 2123 women.Sal-T was measured using liquid chromatography–tandem mass spectroscopy. Linear regression was used to examine associations between health factors and mean Sal-T.In men, mean Sal-T was associated with a range of health factors after age adjustment, and showed a strong independent negative association with body mass index (BMI) in multivariable analysis. Men reporting cardiovascular disease or currently taking medication for depression had lower age-adjusted Sal-T, although there was no association with cardiovascular disease after adjustment for BMI. The decline in Sal-T with increasing age remained after adjustment for health-related factors. In women, Sal-T declined with increasing age; however, there were no age-independent associations with health-related factors or specific heath conditions with the exception of higher Sal-T in smokers.Sal-T levels were associated, independently of age, with a range of self-reported health markers, particularly BMI, in men but not women. The findings support the view that there is an age-related decline in Sal-T in men and women, which cannot be explained by an increase in ill health. Our results demonstrate the potential of Sal-T as a convenient measure of tissue androgen exposure for population research. Sal-T levels in a general population study were associated with BMI in men. An agerelated decline in Sal-T in men and women was found which cannot be explained by an increase in ill-health In men, T deficiency with pituitary or testicular disease  is known to cause a wide range of symptoms and conditions including sexual dysfunction, loss of vigor, poor physical performance, fractures, and low mood, which can be effectively treated with testosterone replacement therapy (TRT) . However2–10–Salivary testosterone  is believed to represent tissue hormone levels, which are unaffected by variations in circulating binding proteins , therebyUsing data from the third National Survey of Sexual Attitudes and Lifestyles , a probability-sample survey of British men and women, we investigated whether Sal-T is associated, independently of age, with demographic characteristics, lifestyle, general health, and reported health conditions. We hypothesized that relationships between Sal-T and health-related factors in men would be similar to those previously observed with serum free-T. To our knowledge, this is the first study to have examined the associations between Sal-T and health in a large community sample of men and women using a highly sensitive and specific assay, exploiting the theoretical and practical advantages of salivary measurements to the full.Full details of the Natsal-3 methods, including details of the saliva sample collection and testing, are described elsewhere , 21. BriSingle morning saliva samples were self collected from a subsample of men and women age 18–74 years who did not regularly work night shifts. Consenting participants were given a self-collection pack and asked to provide their sample before 10:00 hours, to minimize diurnal variation in T (2), these participants were excluded from analysis of BMI (14 men and 44 women). Most of the health questions were asked in the computer-assisted personal interviewing, with the exception of depressive symptoms (past 2 weeks) which were assessed in the computer-assisted self interview using a validated two-item patient health questionnaire (PHQ-2)  was calculated from self-reported height and weight. Due to small numbers of underweight individuals (BMI < 18.5 kg/m (PHQ-2) . CardiacSeason of data collection was included as a potential confounder, defined as: Winter , Spring , Summer , Autumn .The liquid chromatography–tandem mass spectroscopy Sal-T assay was developed using strict validation criteria , with a Statistical analyses were carried out using STATA (version 13.1) accounting for the complex survey design  . We applDescriptive statistics are presented as means (SEs), with multivariable linear regression used to assess differences between groups. Throughout, we censored very high Sal-T values so that, for each 10-year age group stratified by sex, values above the 99th percentile were assigned a value equal to that of the 99th percentile. The Sal-T data for men were normally distributed; however, the distribution for women was positively skewed and so values were transformed on the natural log scale for analysis. Accordingly, for men we present linear regression coefficients representing differences in mean T in pmol/L, whereas for women we present ratios of geometric mean Sal-T obtained from exponentiated coefficients. Interval regression was used to assign values to the range 0 to 6.5 pmol/L for three men, and 0.5  to 6.5 pmol/L for 62 women with T levels below the limit of detection (<6.5 pmol/L). Age was adjusted for using both linear and quadratic terms to account for a nonlinear relationship of T with age.P < .1) with variables selected from earlier domains included with certainty. The ordering of domains began with factors for which the evidence of association was best established (from earlier publications) or of a demographic nature, and then proceeded to health-related factors. In this way, any identified associations between Sal-T and health could be seen as robust and not explained by confounding factors in other domains. An equivalent analysis was not performed for women given the lack of age-adjusted associations. In further analysis we examined associations between specific health conditions or medical treatments and Sal-T, adjusting firstly for age and then for those factors that had been cumulatively selected from domains 1 to 3.Given that several associations were found for men, multivariable analyses were used to determine which health factors were independently associated with Sal-T. Variables were grouped into a series of domains, to identify their individual contributions to the overall relationships with Sal-T after adjustment for earlier domains. The domains were: 1) age and season, 2) relationship status and children, 3) BMI, and 4) general health. A fifth lifestyle domain  contained no significant associations (either age adjusted or multivariable) and was therefore not presented in the final multivariable table. Within each domain the variables were entered into a forward stepwise model selection process . Written informed consent was obtained for anonymized testing of saliva samples, without return of results.For both men and women, mean Sal-T decreased with increasing age, and seasonal variation was observed. Among men, there was variation in mean sal-T by relationship status after adjustment for age, with the highest levels among those who were not currently in a steady relationship, and lowest levels among those who were married or cohabiting ; no association was found with having children. There were no associations with demographic factors for women.Mean Sal-T was associated, independently of age, with a range of measures of general health in men but not in women. In age-stratified analyses of men, mean Sal-T was seen to be lower with increasing BMI  , and somP < .0001). A sensitivity analysis excluding women on HC (n = 499) produced generally similar results, although the association with smoking became nonsignificant due to an increase in the size of the confidence intervals . Adjusting the women's analysis for season as well as age did not change any of the results (data not shown).The only health association found for women was with smoking, with higher Sal-T among women who smoked (ratio of geometric means 1.11 [1.02–1.22] for current smokers compared with nonsmokers). Women who used HC as their usual method of contraception had lower mean Sal-T . In further exploratory analysis we fitted a model excluding BMI but including age, season, and relationship status, in which self-reported general health was found to be more strongly associated with Sal-T .In men, all associations with variables in domains 1–3 in the age-adjusted analyses remained significant in the multivariable analyses: age, season, relationship status, and BMI . Only onP = .119) and diabetes  but strengthened the association with depression medication . There was no evidence of associations between Sal-T and any of these conditions among women.Cardiovascular disease (including hypertension) was reported by 19% of men in our sample, and was associated with lower mean Sal-T in men, independently of age (−18.06 [−29.43 to −6.68]) . There wThis study is the first to show associations between Sal-T and health in a large national probability-sample survey of men and women, across a wide age range. In men, we found significant age-independent associations between lower Sal-T and higher BMI, poorer self-reported general health, mobility problems, longstanding illness, and comorbid conditions . The association between Sal-T and self-reported general health in men was attenuated after adjustment for BMI, suggesting that the relationship is at least partly explained by obesity. We found no associations between Sal-T and health factors in women, except smoking, with higher Sal-T among women who smoked.The present finding of an age-related decline in Sal-T that persisted even after adjusting for health and demographic factors is consistent with previous serum studies that found not only serum total-T, but also serum free-T, declined across an age range in women  and men P = .0932 indicating at best weak evidence of an association, which did not persist after adjusting for other confounding factors including BMI. Although prevalence of diabetes in our sample was similar to national estimates  studies that have reported lower T among men and women in established relationships  and pareWe found no association between Sal-T and smoking, alcohol consumption, or drug use in men. Previous serum-T studies in men have generally, although not always consistently, shown smoking to be associated with increased total-T, and studies of the associations with free-T have yielded mixed results . SmokingPrevious research about the health correlates of T in women has not only yielded inconsistent findings, but has largely been carried out within narrow age ranges, and using suboptimal measures of T . We founOur findings regarding the different relationship with health and obesity for men and women may relate to the different sites of production and mechanisms of regulation. Among women, T is produced from the adrenal glands, regulated by adrenocorticotropic hormone, as well as the ovaries, regulated by gonadotropins, and there are menstrual cyclical fluctuations of ovarian steroids, whereas in men T is produced predominantly from the testes with only a very minor contribution from the adrenals. The mechanisms underlying the relationship between obesity and low T in men remain unclear, although the potential importance of circulating inflammatory cytokines from visceral adipose depots is gaining credence , 40.A key strength of this study is the highly sensitive and specific Sal-T assay, enabling accurate measurement in women as well as men—although there is some systematic positive bias due to salivary protein binding among women —and permThe health data collected were self reported and are therefore reliant on knowledge of conditions and medications, and accurate reporting. This may particularly affect BMI based on self-reported height and weight, given that people tend to underestimate weight and overestimate height. However, previous studies have shown self-reported height and weight to be sufficient for examining associations in epidemiological studies . As a seOnly one sample was collected from each participant and so we were unable to take into account intra-individual variation in T levels, which may be particularly relevant for premenopausal women given that T varies throughout the menstrual cycle . HoweverThe findings presented in this paper provide crucial background for future research into the relationship between Sal-T and sexual function and sexual behavior, as well as being important in their own right for understanding associations between Sal-T and health factors. Our findings are broadly consistent with previous research using serum, and where differences exist it is not always clear whether these are due to differences in the measure used , or due to other differences in the study population and design. Further observational research using reliable saliva T measurements linked to a broader range of clinical correlates would strengthen the evidence base in this respect.There are concerns about inappropriate marketing and use of TRT for men, particularly in the United States . Our croOur finding of an independent age-related decline in Sal-T suggests that reproductive senescence in men, as in women, is not solely the consequence of poor health. The clinical significance of this merits further investigation using Sal-T as well as serum-T measurements. The application of Sal-T measurement in future research should make a significant contribution toward clarifying the role of low T in health and ageing in men and women.


Next-generation sequencing (NGS) technologies have accelerated considerably the investigation into the composition of genomes and their functions. Genotyping-by-sequencing (GBS) is a genotyping approach that makes use of NGS to rapidly and economically scan a genome. It has been shown to allow the simultaneous discovery and genotyping of thousands to millions of SNPs across a wide range of species. For most users, the main challenge in GBS is the bioinformatics analysis of the large amount of sequence information derived from sequencing GBS libraries in view of calling alleles at SNP loci. Herein we describe a new GBS bioinformatics pipeline, Fast-GBS, designed to provide highly accurate genotyping, to require modest computing resources and to offer ease of use.Fast-GBS is built upon standard bioinformatics language and file formats, is capable of handling data from different sequencing platforms, is capable of detecting different kinds of variants . To illustrate its performance, we called variants in three collections of samples  that cover a range of different genome sizes, levels of genome complexity, and ploidy. Within these small sets of samples, we called 35 k, 32 k and 38 k SNPs for soybean, barley and potato, respectively. To assess genotype accuracy, we compared these GBS-derived SNP genotypes with independent data sets obtained from whole-genome sequencing or SNP arrays. This analysis yielded estimated accuracies of 98.7, 95.2, and 94% for soybean, barley, and potato, respectively.We conclude that Fast-GBS provides a highly efficient and reliable tool for calling SNPs from GBS data. Currently, genomics lies at the heart of an extraordinary number of discoveries, innovations and applications. This revolution is a direct result of the rise of next-generation sequencing (NGS) technologies –4. In thAdvanced sequencing technologies (NGS) have reduced both the cost and the time required to generate sequence data. The efficient and accurate computational processing, variant and genotype calling of large-scale NGS data is the new bottleneck in genomics. To meet this need, numerous bioinformatics pipelines have been developed –16 and ade novo-based and reference-based. In the presence of a reference genome, the reads from reduced-representation sequencing can be mapped to the reference genome and SNPs can be called [de novo-based approach are UNEAK and Stacks [Conventionally, bioinformatics pipelines for handling GBS data are categorized in two groups: e called , 20. Up e called –15, 21. d Stacks .Herein, we describe a new reference-based pipeline, Fast-GBS, and we benchmark the pipeline based upon a large-scale, species-wide analysis of soybean, barley and potato. It is easy to use with various species, in different contexts, and provides an analysis platform that can be run with different types of sequencing data and modest computational resources.To test the performance of Fast-GBS, we used existing sequence datasets for panels of 24 unrelated accessions/clones for three species covering a range of genomic situations: soybean , barley To estimate genotype accuracy for Fast-GBS calls, we compared the called SNPs with independently derived genotypic data resulting from either whole-genome resequencing (soybean and barley) or genotyping on a SNP array (potato) for the same samples. For soybean, we compared the GBS-called SNPs with whole genome resequencing data for the same 24 samples. In the case of barley, GBS-derived genotypic data for one of the 24 barley samples (cv. Morex) was compared to the barley reference genome produced using this same cultivar. For potato, we compared the GBS-derived genotypes with those obtained for the same 24 samples at a set of 122 SNPs that were in common with the SolCAP Infinium Chip (8.3 k SNPs) .The Fast-GBS analysis pipeline was developed by integrating public packages with internally developed tools. The public packages include Sabre (demultiplexing) , CutadapWe developed a Bash script to create the directory structure before running the Fast-GBS pipeline. This command line creates the directories for data (FASTQ files), barcodes (key file), reference genome, and results (Fast-GBS outputs).The input data are sequenced DNA fragments from any restriction enzyme–based GBS protocol. Fast-GBS handles raw sequencing data in FASTQ format.The parameter file is a text file containing key information about the analysis including the path to the FASTQ files, barcodes and reference genome. It also contains information about the type of sequence (paired or single-end), the adaptor sequence and the sequencing technology. In this file we can define critical filtering options such as the minimal quality scores for reads, minimal number of reads required to call a genotype, and maximal amount of missing data allowed. Number of CPU, names of output files are also defined in this file. This file comes with the Fast-GBS pipeline.The cost efficiency of GBS is partly due to the multiplexing of samples and the resulting pooled reads will need to be demultiplexed prior to SNP calling. Fast-GBS uses Sabre  to demulAfter demultiplexing, Fast-GBS uses Cutadapt to find and remove adapter sequences, primers, and other types of unwanted sequence from high-throughput sequencing reads .Fast-GBS uses the MEM  algorithm implemented in BWA that works by seeding alignments and then extending seeds with the Smith-Waterman (SW) algorithm using an affine gap penalty . This alAfter initial alignment, the mapped reads are further processed by Platypus  in orderIn Fast-GBS, variants are called using Platypus. Unlike alignment-based variant callers which focus on a single variant type (SNP or indel), Platypus uses multi-sample variant calling that helps to exploit information from multiple samples to call variants that may not look reliable in a single sample. This approach decreases the errors around indels and larger variants (MNPs). At first, the local assembler looks at a small window (~few kb) at a time and uses all the reads in the window to generate a colored de Bruijn graph, then using all candidate variants, it generates an exhaustive list of haplotypes. Candidate haplotypes are generated by clustering the candidate alleles across windows. Haplotype frequencies are estimated by the expectation-maximization (EM) algorithm. Then variants are called using the estimated haplotype frequencies. This approach works on the local haplotype level rather than on the level of individual variants and does well on highly divergent regions. This also decreases computational requirements.Platypus was originally designed and used to detect variants in human, mouse, rat and chimpanzee samples. To optimize Platypus options in the context of the analysis of GBS-derived single-end reads, we modified several options  derived from a 24-plex MspI/PstI library. Finally, in potato, 38 k SNPs were obtained from sequencing a 24-plex MspI/PstI library (43 million 100-bp Illumina reads).To assess the performance of the Fast-GBS analysis pipeline, we used it to analyze existing GBS-derived read data from sets of 24 soybean, barley, and potato samples. Table GBS was originally demonstrated for soybean by Sonah et al  using thMspI/PstI-digested library) and they called 34 k and 19 k SNPs using either the reference genome (with SAMtools) or a de novo pipeline (TASSEL), respectively. In this study we used Fast-GBS for SNP calling in barley and, as can be seen in Table Barley has one of the larger genomes (>5 Gb) among cultivated plant species. Because of the huge size and high level of complexity of its genome, complexity reduction is highly recommended in barley, an important crop species for which a draft genome has been published . MascherBecause of the high level of ploidy and heterozygosity, potato is a challenging species for genotyping. The most often used method for genotyping in potato is a SNP array. Two SNP arrays have been developed so far, the SolCAP 8 k and 20 k arrays , 34, 35.An important aspect to consider for any variant calling tool is the accuracy of called genotypes. In this study, we estimated the accuracy of genotypes called by Fast-GBS Table  by compaIn this study, to assess the performance of Fast-GBS, we used both Illumina and Ion Torrent reads. Soybean and potato samples were sequenced using an Illumina Hiseq platform and barley samples on an Ion Torrent (Proton) platform. Typically for GBS, Illumina sequencing generates reads of uniform length (100 bp), while Ion Torrent reads are in 50 to 150 bp. Ion Torrent sequencing usually leads to a higher rate of sequencing errors , 39. ThuGBS provides an extremely powerful and versatile tool for identifying and calling genetic markers to be used by researchers working in numerous species and fields of study. This genotyping approach, like all applications based on NGS, generates a huge amount of raw data. These data need to be analyzed as quickly and efficiently as possible, all the while yielding SNP data that is highly accurate. Fast-GBS showed itself to be a powerful pipeline to generate large numbers of highly accurate SNPs using sequence read data obtained from different sequencing platforms and diverse species characterized by different levels of ploidy, zygosity, and genome complexity. By combining efficiency and accuracy in this way, Fast-GSB constitutes a useful tool for a broad array of users in different research communities.Project name: Fast-GBSProject home page:https://bitbucket.org/jerlar73/fast-gbsOperating system: LinuxProgramming language: Bash and PythonLicense: GNU GPL vAny restrictions to use by non-academics: NoSequence data are available in NCBI Sequence Read Archive (SRA) with the SRP# Study accession, SRP059747.


Interference resolution refers to cognitive control processes enabling one to focus on task-related information while filtering out unrelated information. But the exact neural areas, which underlie a specific cognitive task on interference resolution, are still equivocal. The multi-source interference task (MSIT), as a particular cognitive task, is a well-established experimental paradigm used to evaluate interference resolution. Studies combining the MSIT with functional magnetic resonance imaging (fMRI) have shown that the MSIT evokes the dorsal anterior cingulate cortex (dACC) and cingulate–frontal–parietal cognitive-attentional networks. However, these brain areas have not been evaluated quantitatively and these findings have not been replicated.In the current study, we firstly report a voxel-based meta-analysis of functional brain activation associated with the MSIT so as to identify the localization of interference resolution in such a specific cognitive task. Articles on MSIT-related fMRI published between 2003 and July 2017 were eligible. The electronic databases searched included PubMed, Web of Knowledge, and Google Scholar. Differential BOLD activation patterns between the incongruent and congruent condition were meta-analyzed in anisotropic effect-size signed differential mapping software.Robustness meta-analysis indicated that two significant activation clusters were shown to have reliable functional activity in comparisons between incongruent and congruent conditions. The first reliable activation cluster, which included the dACC, medial prefrontal cortex, supplementary motor area, replicated the previous MSIT-related fMRI study results. Furthermore, we found another reliable activation cluster comprising areas of the right insula, right inferior frontal gyrus, and right lenticular nucleus-putamen, which were not typically discussed in previous MSIT-related fMRI studies.The current meta-analysis study presents the reliable brain activation patterns on MSIT. These findings suggest that the cingulate-frontal-striatum network and right insula may allow control demands to resolve interference on MSIT. These results provide new insights into the neural mechanisms underlying interference resolution. The interjection of goal-irrelevant information with goal-relevant information is referred to as cognitive interference. For instance, while trying to concentrate on your job, you may have to inhibit the habitual tendency to check your Facebook feed. Successful interference resolution depends on flexible cognitive control that suppresses goal-irrelevant inputs, while selecting and organizing goal-relevant inputs.congruent condition  and is in conflict with its correct button-press response in the incongruent condition . In the MSIT, an interference effect is indexed by the difference in reaction time between incongruent and congruent conditions.The multi-source interference task (MSIT) is a cognitively demanding well established paradigm for assessment of cognitive interference. In the MSIT, stimuli  are organized into groups of three and participants are required to recognize a unique target among the three items under congruent and incongruent conditions [In an initial pilot imaging study of MSIT performance, Bush et al. reported that the dorsal anterior cingulate cortex (dACC) was reliably activated at either the individual- or group-level in the incongruent condition, compared with congruent condition, indicating that the dACC is important for interference processing . LikewisCingulate-frontal-parietal (CFP) cognitive-attentional networks have also been reported to be widely and significantly activated by MSIT , 12. In The MSIT interference effects on cortical activity in the aforementioned studies were variable, perhaps due to differences in study design and sample characteristics. Hence, a quantitative assessment of brain network activity in MSIT is needed. In the present study, we applied a meta-analytic approach to synthesize the published MSIT-fMRI studies with the aim of clarifying the locations of generators of interference processing during MSIT performance. We used effect-size signed differential mapping (ES-SDM) as the meta-analytic toolbox –22. The http://www.pubmed.org), Web of Knowledge (http://apps.webofknowledge.com), and Google Scholar (http://scholar.google.com) for MSIT-related fMRI studies from 2003 to July 2017. The search term combinations used were: “multi-source interference task” and “functional magnetic resonance imaging”. A total of 603 papers were found and assessed to determine if they met the following criteria: (1) an original article published in a peer-reviewed English-language journal; (2) a study employed MSIT during fMRI with a healthy control group; (3) the BOLD fMRI technique was used; (4) MSIT stimuli were numbers and MSIT trials included both incongruent and congruent conditions, as in Fig. We conducted a systematic search of PubMed (http://www.sdmproject.com). ES-SDM, which is a voxel-based meta-analytic approach, is described in detail in the SDM tutorial and publications  [Differential BOLD activation patterns between the incongruent and congruent condition were meta-analyzed in Anisotropic Effect-Size Signed Differential Mapping (ES-SDM) software, version 4.13  , 22, 23.z-values, where z could be a positive z-statistic or a negative z-statistic. Second, effect-size and effect-size-variance maps were recreated for each study. Anisotropic kernels were used to optimize the accuracy of these maps [p < 0.00001 and a cluster-level (extent) threshold of k = 100 voxels [The meta-analysis procedure followed three steps. First, the peak coordinates of brain activation differences between incongruent and congruent conditions were retrieved from each study. Peak coordinates were recorded with their ese maps . Activatese maps . Third, ese maps , 22. The0 voxels .To evaluate the robustness and replicability of meta-analytic results, whole-brain-voxel-based Jackknife sensitivity analysis was conducted, wherein the same meta-analysis is repeated nine times, each time with a different single study excluded. The principle of the procedure is that if the previous meta-analytic results remain significant, the results can be considered robust and reliable , 23. Stap < 0.005 and a cluster-level threshold of k = 10 voxels [Employing a random effects model with Q statistics, we analyzed heterogeneity to determine whether the observed inter-study variance was larger than that resulting from sampling error alone , 23. Suc0 voxels .A subgroup analysis of adult samples was conducted to examine if potential confounding effects of age contributed to the heterogeneity of the findings , 23. To In total, 20 studies met the inclusion criteria for our meta-analysis, of which 12 were excluded for overlapping or duplicating data, leaving eight studies eligible for the final meta-analysis. One of these involved two different healthy sample populations (an adult sample and a youth sample), and the interference effect results of each of the two samples were treated as an independent dataset in the meta-analysis . Hence, The characteristics of the analyzed MSIT-fMRI studies (nine datasets) are summarized in Table Voxel-wise meta-analysis showed that, compared to the congruent condition, the incongruent condition produced significantly increased activity in three clusters, involving the dACC, medial prefrontal cortex (MPFC), supplementary motor area (SMA), right insula, right inferior frontal gyrus (IFG), right lenticular nucleus-putamen (PUT), left precentral gyrus, and left IFG Table , Fig. 2.As reported in Table To our knowledge, this is the first report of a voxel-based meta-analysis that identified MSIT-associated functional brain activation. Robustness analyses confirmed that the significance of two major activation clusters involving the dACC, MPFC, SMA, right insula, right IFG, and right PUT was reliable and robust during comparison between incongruent and congruent conditions.Our findings are consistent with previous fMRI studies on MSIT indicating robust activation in the dACC, MPFC and SMA during interference processing when incongruent and congruent conditions are compared , 11, 28.An unexpected finding in our meta-analysis was a significantly active cluster involving the right IFG, right insula, and right PUT in comparisons between incongruent and congruent conditions. But previous studies employing the MSIT have found that CFP cognitive-attentional networks are reliably activated under these conditions. Although the result was not predicted, it is in agreement with a previously proposed role of the right IFG . In a syThe insula is a commonly activated region in the go/no-go task, flanker task, and stimulus–response compatibility task, and insula activation has been shown to be related to interference resolution in each task . Cai et In summary, our findings extend the results of prior MSIT studies, confirming that the dACC and prefrontal cortex are the main brain areas activated by MSIT performance. Our meta-analysis confirms cogently, for the first time, two robust activation clusters encompassing the dACC, MPFC, SMA, right IFG, right PUT, and right insula during MSIT performance. Compared to the congruent condition in the MSIT, the incongruent condition is characterized by more conflict and a greater need for cognitive control. On the basis of the functions of the aforementioned brain regions, we postulate that the right insula may send saliently relevant (high interference) signals to the dACC to be used to induce conflict monitoring, and to the SMA, right IFG, and PUT to be used for movement planning and inhibitory control, enabling goal-related flexible, adaptive behavior to be established. Hence, our findings indicate that a cingulate-frontal-striatum network and the right insula may serve as a critical brain circuit in interference resolution.


FVI was measured by the National Cancer Institute’s (NCI) Fruit and Vegetable Screener (FVS) and an inventory of locally grown fruits and vegetables. FVI relative to United States (US) recommendations and averages, and across seasons, were tested with non-parametric tests and paired t-tests (p < 0.05). Both adults and children in the CO-CSA had higher FVI than the US averages, and more often met recommendations for vegetables. Some summer fruits and vegetables were more often eaten when locally in-season. The CO-CSA model warrants further examination as an avenue for improving vegetable consumption among adults and children in low-income households. However, causality between CO-CSA participation and FVI cannot be inferred, as CO-CSA participants may be positive deviants with respect to FVI. A multi-state randomized controlled trial is currently underway to evaluate impacts of CO-CSAs on FVI and related outcomes.This paper examines fruit and vegetable intake (FVI) in low-income households that participated in a cost-offset (CO), or 50% subsidized, community-supported agriculture (CSA) program. CSA customers paid farms upfront for a share of the harvest, and received produce weekly throughout the growing season. A cohort of adults and children 2–12 y in a summer CO-CSA were surveyed online twice: August 2015 ( Eating a diet rich in fruits and vegetables is associated with the prevention of poor health outcomes in adults ,2,3. AltRecent research suggests that shopping at farmers’ markets is positively associated with FVI ,19,20, aCommunity supported agriculture (CSA) is one mechanism that may improve access to fresh produce for low-income households. In CSAs, customers pay for a ‘share’ of produce before the growing season begins, and farmers provide fruits and vegetables weekly throughout the season ,31,32,33In this study, we compared FVI for adults and children from households that participate in a CO-CSA with US dietary recommendations and averages, and hypothesized that CO-CSA participants would have higher FVI. We also contrasted total FVI during the summer CO-CSA season and in the winter (without the CO-CSA) and expected that participants would have higher FVI during the summer CO-CSA than in the winter. Third, we examined seasonal variation in the varieties of fruits and vegetables consumed by CO-CSA participants, and hypothesized that produce varieties that were in-season would be consumed more frequently than those out of season. Examining FVI among adults and children that participate in a CO-CSA will add to our understanding of the potential for CSAs to support positive dietary change for members of low-income and food insecure households.Design and Setting. This paper reports on a longitudinal survey of adults and children who participated in a CO-CSA program operated by the Northeast Organic Farming Association of Vermont (NOFA-VT) in the US . The NOFA longitudinal survey was conducted in the summer (August 2015) and again the following winter (February 2016). All participants were already enrolled in the NOFA-VT CO-CSA at the summer survey. Participants in the winter survey reported they were not participating in any type of CSA. Institutional Review Boards at Cornell University and the University of Vermont approved the study protocol, and consent was obtained electronically. n = 85), did not obtain a CO-CSA (n = 12), or who did not provide an email address (n = 1) were excluded. The remaining 81 households were invited to the summer online survey. Summer survey participants were subsequently invited to complete the winter survey. Participants were compensated $25 for each survey they completed.Participants. Names and contact information for all 179 low-income NOFA-VT CO-CSA applicants for summer 2015 were obtained, and households that did not report a child aged 2–12 years , indicators of meeting or exceeding recommendations, and frequencies of consuming particular fruits and vegetables (times per month). The child’s dietary data were generally reported by the parent who prepared most of the child’s meals, reporting either with the child (35%) or alone (58%). FVI was assessed with the NCI All-Day Fruit and Vegetable Screener (FVS). The validated FVS collected the frequency and usual portion size for nine fruit and vegetable components  in the past month . We formFor 16 varieties of vegetables and 12 fruits that were locally grown and only seasonally available ,51, freqHousehold, respondent, and child characteristics were collected as part of the summer survey. Participants provided a household roster from which number of adults and children, sex and age of the respondent, and sex and age of the focal children were recorded. Household food security was classified by the 6-item short form of the USDA Food Security Survey Module (FSSM), with a 30-day reference period . Two queStatistical Methods. Sample characteristics were summarized with frequencies and percentages using SPSS version 23 software . US mediForty-one CO-CSA participants responded to the summer survey (50.6%). Most participant households included two adults (71.0%) and multiple children 75.6%; . More thp < 0.01; p < 0.01). Notably, 81.6% of adults and 82.9% of children in CO-CSA participant households met DGA recommendations for vegetable intake.Both adults and children in CO-CSA households consumed more fruits and vegetables than the US median . Median total FVI in the summer and winter did not significantly differ for adults (6.44 vs. 6.39 cups/day) or children . However, patterns of seasonality emerged in the types of fruits and vegetables consumed . When loCO-CSA participants and their children reported total FVI greater than the US average, and more often met recommendations for vegetable consumption than the US population. They also more often consumed some summer vegetables and fruits when locally in-season than when out-of-season. Our findings are consistent with prior studies that found adult CSA members consumed a larger quantity of fruits and vegetables than their non-CSA counterparts ,39,40,41While these data suggest higher-than-expected FVI among low-income CO-CSA participants, we cannot infer causality between CO-CSA participation and FVI from these observational data. Although all the CO-CSA participants had low-incomes, the majority of respondents were highly educated, which suggests that they were atypical of the US population with low-incomes. Passive recruitment approaches may have contributed to the selection of motivated and atypically educated participants. Education is known to be positively associated with healthy dietary behaviors such as vegetable consumption, which further introduces selection bias. Consistently high FVI reported in summer and winter (time points with and without the CO-CSA) supports the likelihood that selection bias contributed, at least in part, to the high levels of FVI reported for adults and children in CO-CSA households.Low-income households that participate in CO-CSAs may be ‘positive deviants’ with respect to FVI. Positive deviants are at-risk members of a population whose uncommon practices enable them to achieve better outcomes than their peers who share similar risks . In thisCO-CSAs warrant further examination as an avenue to improving vegetable consumption among adults and children in low-income households. A multi-state randomized controlled trial is currently underway to evaluate impacts of CO-CSA participation on FVI, food security, and related outcomes.