is there any limitation to the input document text size ?

[SundeepPidugu]

I was trying to run the demo with a huge document text and it shows me There was an error generating a question :( is there any limitation for the document text ? when i run the same with this repo ?

[tomhosking]

The model truncates the input to the model to a window of approx 200 tokens around the answer, so a long document shouldn't matter. That error usually happens when the system can't find the answer within the document provided - note that this is case sensitive.

[SundeepPidugu]

@tomhosking got it let me try it with the exact answer in the document

[SundeepPidugu]

@tomhosking had the exact same phrase in the document as the answer but still was not able to generate a question ? is there any basic preprocessing that should on top of the text document ?

[tomhosking]

Can you post the document and answer here?

[SundeepPidugu]

document text

kim et al. nutrition metabolism nutrition metabolism doi . s research open access replacing carbohydrate with protein and fat in prediabetes or type diabetes greater effect on metabolites in peripheral blood mononuclear cells than plasma minjoo kim , gayoung song , , miso kang , , hye jin yoo , , tae sook jeong , sang hyun lee and jong ho lee , , abstract background active metabolism of peripheral blood mononuclear cells could suggest their suitability for metabolomics studies. this study examined whether reductions in peripheral blood mononuclear cells s and plasma lipoprotein associated phospholipase a lp pla activities induced by dietary intervention affected the overall metabolic profiles of peripheral blood mononuclear cells and plasma. methods eighty nonobese subjects aged years . bmi kg m with prediabetes or newly diagnosed type diabetes were assigned to consume either the usual refined rice diet control group, n or to replace refined rice with whole grains and legumes as carbohydrates whole grain group, n for three meals per day during the week intervention. fasting peripheral blood mononuclear cells and plasma metabolomes were profiled using uplc ltq orbitrap mass spectrometry. results after weeks, changes in fasting glucose, hba c, homeostasis model assessment insulin resistance , malondialdehyde , ox low density lipoprotein , low density lipoprotein particle size, plasma lp pla activity, and peripheral blood mononuclear cells enzyme activity in the whole grain group were significantly different from those in the control group before and after adjusting for baseline levels. the peripheral blood mononuclear cells levels of l leucine, oleamide, lysopc , and lysopc in the whole grain group showed greater reductions compared with those of the control group. changes in plasma metabolites were not significantly different between the two groups. changes in peripheral blood mononuclear cells lp pla activity positively correlated with changes in l leucine, oleamide, lysopc , lysopc , glucose, and ox low density lipoprotein , and negatively correlated with changes in low density lipoprotein particle size. conclusions this study showed that dietary intervention in prediabetic or type diabetic patients had a greater effect on peripheral blood mononuclear cells lp pla activity and metabolites compared with those of plasma metabolites. trial registration nct keywords metabolites, peripheral blood mononuclear cells, prediabetes, whole grains and legumes kim et al. open access this article is distributed under the terms of the creative commons attribution . international license http creativecommons.org licenses by . , which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author and the source, provide a link to the creative commons license, and indicate if changes were made. the creative commons public domain dedication waiver http creativecommons.org publicdomain zero . applies to the data made available in this article, unless otherwise stated. background diabetes is an epidemic metabolic disorder about . million korean people . aged years or older had type diabetes and . of adults had prediabetes in according to korean diabetes fact sheet . diabetes related mortality was steadily decreased since and ranked as the fifth leading cause of natural death . prediabetes can be indicated by either impaired fasting glucose by the american diabetes association criteria or impaired glucose tolerance by world health organization criteria . lipoprotein associated phospholipase a lp pla independently predicts type diabetes incidence and may be involved in its etiology . in recent study, an inverse association was observed between protein intake and circulating lp pla activity, suggesting that nutritional factors may influence lp pla activity . an intervention study that replaced refined rice with whole grains and legumes reduced blood glucose, insulin, lp pla activity, and cardiovascular risk factors in patients with prediabetes or type diabetes . the effects of this intervention diet on plasma and peripheral blood mononuclear cell metabolites have not been determined. peripheral blood mononuclear cells s include monocytes and lymphocytes which are blood cells having a round nucleus. these blood cells are a critical component in the immune system to fight infection and adapt to intruders. monocytes have a key role in onset and development of inflammatory reactions by generating bioactive molecules such as lp pla in response to inflammatory stimuli . lymphocytes are consist of three major types t cells, b cells, and natural killer cells. t cells and b cells are the major cellular components of the adaptive immune response, whereas natural killer cells are a part of the innate immune system. the production and release of lp pla by lymphocytes may become increased under inflammatory conditions . dietary intervention induces peripheral blood mononuclear cells gene expression changes, including downregulating genes involved in inflammatory processes . therefore, changes in peripheral blood mononuclear cells metabolites and lp pla activity after dietary intervention could reflect dynamic responses, which are not detectable in plasma metabolomics analyses. the aim of this week intervention study was to examine whether reductions in peripheral blood mononuclear cells and plasma lp pla activities induced by dietary intervention replacement of refined rice with whole grains and legumes, and higher intake of vegetables affected the overall metabolic profiles of peripheral blood mononuclear cells and plasma in nonobese patients that exhibited impaired fasting glucose , impaired glucose tolerance , or newly diagnosed type diabetes . methods subjects and study design nonobese subjects aged years . bmi kg m were recruited from the health service center at the ilsan hospital, goyang, korea, during january june . based on the health service center data, subjects who had impaired fasting glucose fasting glucose mg dl or newly diagnosed type diabetes fasting glucose mg dl were referred to the department of family medicine or internal medicine. exclusion criteria included current and or past history of cardiovascular disease liver or kidney dysfunction thyroid or pituitary disease. subjects who were taking medications or supplements also were excluded. a total of subjects were enrolled. the macronutrient composition of each subject's usual diet corresponded to a typical diet with cooked refined rice. the purpose of the study was carefully explained to all participants, and written consent was obtained prior to their participation. the institutional review board of the nhic sponsored ilsan hospital and yonsei university provided ethical approval of the study protocol, which was performed according to the helsinki declaration. the present study was performed in two phases, including a week run in phase consisting of the usual diet with refined rice, and a week intervention phase. during the run in period, two subjects who did not maintain their energy intake dropped out. the remaining subjects were randomly subdivided into the two study groups, and were assigned to consume either the usual refined rice diet control group, n or to replace refined rice with whole grains and legumes as carbohydrates whole grain group, n for three meals per day during the week intervention. assessment of dietary intake and physical activity level all subjects were given written and verbal instructions by a registered dietitian on completion of a day dietary record every weeks throughout the study. on the dietary record sheet, subjects were instructed to weigh and record the food amount before and after ingestion. all participants were advised to continue their usual refined rice diet during a week run in period. baseline measurements were performed at the start of the run in phase. after a run in period, subjects in the control group maintained the usual refined rice diet, whereas subjects in the whole grain group replaced refined rice with a mix of legumes, barley, and wild rice three times per day, and increased vegetable intake to at least units g unit per day for sufficient dietary fiber intake. the dietitian monitored subject compliance and body weight changes during the whole study by performing biweekly visits or telephone interviews and all participants were encouraged to maintain their usual lifestyles. dietary energy values and nutrient contents from day food records were calculated using the can pro . korean nutrition society, seoul, korea . total energy expenditures kcal day were calculated from activity patterns including basal metabolic rate, physical activity for h , and specific food dynamic action. basal metabolic rate for each subject was calculated with the harris benedict equation . anthropometry and blood pressure analysis body weight and height of unclothed subjects without shoes were measured in the morning for calculating body mass index bmi, kg m . waist circumference was measured on standing subjects at the umbilical level after normal expiration. blood pressure of seated subjects after a min rest was measured in the left arm with an automatic blood pressure monitor ft s, jawon medical, gyeongsan, korea . after a h fasting period, venous blood specimens were collected in edta treated and plain tubes and centrifuged to yield plasma or serum, respectively, which were stored at degc until analysis. clinical measurements fasting total cholesterol and triglyceride levels were analyzed using a hitachi autoanalyzer hitachi ltd., tokyo, japan . apob containing lipoproteins were precipitated with dextran magnesium sulfate, and high density lipoprotein cholesterol concentrations in patient serum samples were measured enzymatically. for subjects with serum triglyceride levels mg dl, low density lipoprotein cholesterol concentrations were estimated indirectly using the friedewald formula. for subjects with serum triglyceride levels mg dl, low density lipoprotein cholesterol concentrations were measured directly. free fatty acids were analyzed using the acyl coa synthetase acyl coa oxidase enzymatic assay method and a hitachi autoanalyzer. all subjects underwent an oral glucose tolerance test at and weeks by ingesting a g glucose solution after a h overnight fast. venous specimens were collected before glucose loading, at loading, and , , and min after loading to determine serum glucose levels and responses. fasting glucose levels were analyzed by the hexokinase method using a hitachi autoanalyzer. insulin levels were measured using an immunoradiometric assay kit from diasource immunoassays s.a. louvain, belgium . hemoglobin a c was measured by immonoturbidimetric analysis. insulin resistance was calculated by the homeostasis model assessment . whole blood was mixed with the same volume of rpmi gibco, life technologies, gland island, ny and gently laid on a histopaque sigma aldrich, st. louis, mo . the sample was then centrifuged at rpm for min at degc. after the separation, a thin layer of peripheral blood mononuclear cells s was isolated and washed twice with rpmi . the pellet was resuspended in rpmi with streptomycin. isolated peripheral blood mononuclear cells s were cultured in rpmi supplemented with fetal bovine serum , seeded in well plates x cells ml spl, gyeonggi do, korea , and incubated at degc with co for . h. after a . h incubation, fetal bovine serum was added and incubated for . h. at third day, peripheral blood mononuclear cells supernatants were collected and stored at degc until lp pla activity levels were assayed. lp pla activity in plasma and peripheral blood mononuclear cells supernatants was measured by using a modification of a previously described high throughput radiometric activity assay . serum high sensitivity c reactive protein hs crp was measured with an advia clinical chemistry system siemens ltd., tarrytown, ny using a commercially available, hs crp latex x kit denka seiken co., ltd., tokyo, japan . plasma malondialdehyde was measured from thiobarbituric acid reactive substances using the thiobarbituric acid reactive substances assay kit zeptometrix co., buffalo, ny . low density lipoprotein particles were isolated by sequential flotation ultracentrifugation, and particle size distribution . . g ml was examined using a pore gradient lipoprotein system cbs scientific company, san diego, ca on commercially available, non denaturing gels containing a linear acrylamide gradient . latex bead conjugated thyroglobulin , ferritin , and catalase standards were used to estimate the relative band migration rates. gels were scanned using a gs calibrated imaging densitometer bio rad laboratories, hercules, ca . plasma oxidized low density lipoprotein was measured using an enzyme immunoassay mercodia ab, uppsala, sweden , and the resulting color reaction was determined at nm on a wallac victor multilabel counter perkin elmer life sciences, boston, ma . global metabolic profiling of peripheral blood mononuclear cells and plasma peripheral blood mononuclear cells and plasma extract sample preparation before analysis, ml of acetonitrile was added to ml of peripheral blood mononuclear cells and plasma, mixed by vortexing, and centrifuged at , rpm for min at degc. the supernatant was dried with n , dissolved in methanol, mixed by vortexing, and centrifuged at , rpm for min at degc. the supernatant was transferred into a vial. ultra performance liquid chromatography peripheral blood mononuclear cells and plasma extract samples were injected into an acquity uplc beh c column . x mm, . mm waters, milford, ma that was coupled in line with a uplc ltq orbitrap xl thermo fisher scientific, waltham, ma . the injected samples were equilibrated with water containing . formic acid. samples were eluted with an acetonitrile gradient containing . formic acid at a flow rate of . ml min for min. metabolites were separated by uplc, analyzed, and assigned by ltq orbitrap xl. the mass spectrometer was operated in esi positive mode. the spray voltage was kv. the flow rate nitrogen sheath gas and the auxiliary gas were and . the capillary voltage , tube lens voltage , and capillary temperature were kept constant at v, v, and degc. orbitrap data were collected in the range of m z , . mass spectrometer mass spectrometer spectra of metabolites were obtained by a collision energy ramp from ev, and conducted with xcalibur . and mass spectrometer frontier software . data processing and identification of metabolites all mass spectrometer data including retention times, m z, and ion intensities were extracted by sieve software incorporated into the instrument, and the resulting mass spectrometer data were assembled into a matrix. sieve parameters were set as follows m z range , m z width . retention time width . and m ztolerance . . metabolites were searched using the following databases chemspider , human metabolome , lipid maps , kegg www.genome.jp kegg , and massbank . selected metabolites were confirmed by retention times and mass spectra of standard samples. statistical analyses statistical analyses were performed using spss v. . ibm spss statistics , chicago, il . skewed variables were logarithmically transformed for statistical analyses. a two tailed p value of . was considered statistically significant. differences in biochemical variables between two groups at baseline and follow up were tested using student's independent t test. general linear model tests were applied to compare parameter changes between the two groups by adjusting for baseline values. paired t tests were used to evaluate differences between baseline and follow up levels in each group. pearson's and partial correlation coefficients were used to examine the relationships between variables over time. false discovery rate corrected q values were computed using the r package 'fdrtool'. heat map was created to visualize and evaluate correlations among metabolites and conventional risk factors in study populations. multivariate statistical analysis was performed using simca p software version . umetrics, umea, sweden . partial least squares discriminant analysis pls da was used as the classification method for modeling the discrimination between groups by visualizing the score scatter plot or s plot using the first and second pls components. the goodness of fit was quantified by r y, whereas the predictive ability was quantified by q y. generally, r y describes how well the data in the training set were mathematically reproduced and varied between and . models with q y . were considered to have good predictive capabilities. results clinical characteristics, lipid profiles, and nutrient intake there were no significant differences between two groups in baseline characteristics including age, gender, smoking, and drinking . at baseline, there were no significant differences between two groups in bmi, waist hip ratio , systolic blood pressure , diastolic blood pressure , serum triglyceride, total cholesterol, low density lipoprotein cholesterol, high density lipoprotein cholesterol, free fatty acids , and hs crp. bmi, waist hip ratio , blood pressure , serum lipid profiles, hs crp, total energy expenditure, and total energy intake were similar before and after the study in both groups . replacement with whole grains and legumes caused significant increase in percent energy intake of protein and fat, and significant decrease in percent energy intake of carbohydrate. the percent energy intake of protein, fat, and carbohydrate significantly differed between the two groups before adjusting for baseline values. the whole grain group had significant increases in fiber intake and polyunsaturated to saturated fatty acids ratio compared with baseline values. after week, the whole grain group had lower percent energy of carbohydrate, higher percent calorie of protein and fat, and fiber intake than control group . mean sem. . tested by logarithmic transformation, p a , values derived from independent t test in baseline. p b , values derived from independent t test in follow up. p c , values derived from independent t test in changed value. p d , values derived from independent t test in changed value after adjusting for baseline. p . , p . , p . derived from paired t test. peripheral blood mononuclear cells , peripheral blood mononuclear cell auc, area under the curve pufa sfa, polyunsaturated to saturated fatty acids ratio fasting glucose, insulin, and malondialdehyde at the end of the study, glucose, hba c, and malondialdehyde concentrations significantly increased in the control group, whereas glucose, glucose auc , hba c, homeostasis model assessment insulin resistance , insulin, and malondialdehyde significantly decreased in the whole grain group . changes in glucose, glucose auc, hba c, homeostasis model assessment insulin resistance , and malondialdehyde in the whole grain group were significantly different from those in the control group before and after adjusting for baseline levels. post treatment glucose, homeostasis model assessment insulin resistance , and malondialdehyde in the whole grain group were significantly lower than those in the control group . plasma ox low density lipoprotein , low density lipoprotein particle size, lp pla activity in plasma and unstimulated peripheral blood mononuclear cells at the end of the study, the whole grain group had lower ox low density lipoprotein and lp pla activity in peripheral blood mononuclear cells and larger low density lipoprotein particle size, whereas the control group had higher lp pla activity in peripheral blood mononuclear cells . these changes in ox low density lipoprotein , low density lipoprotein particle size, plasma lp pla activity, and peripheral blood mononuclear cells lp pla activity in the whole grain group were significantly different from those in the control group before and after adjusting for baseline levels. the post treatment whole grain group had lower ox low density lipoprotein and peripheral blood mononuclear cells lp pla activity, and larger low density lipoprotein particle size than control group . metabolic profiling of peripheral blood mononuclear cells and plasma using uplc ltq orbitrap mass spectrometer nontargeted metabolic pattern analysis mass spectrometer data of peripheral blood mononuclear cells and plasma metabolites obtained at baseline and follow up were analyzed with pls da score scatter plot for the following two combinations control and whole grain groups at baseline, control group at follow up, and whole grain group at follow up fig. a, peripheral blood mononuclear cells fig. c, plasma and control and whole grain groups at follow up fig. b, peripheral blood mononuclear cells fig. d, plasma . the peripheral blood mononuclear cells metabolite pls da score scatter plot showed distinct clustering and clear separation for the following subjects control and whole grain groups at baseline, control group at follow up, and whole grain group at follow up r x . , r y . , q y . . these distinct clusters indicate that peripheral blood mononuclear cells profiling detects metabolic changes induced by dietary intervention. the peripheral blood mononuclear cells metabolite pls da score scatter plot showed distinct clustering for control and whole grain groups at follow up r x . , r y . , q y . . fig. identification of peripheral blood mononuclear cells and plasma metabolites that were significantly altered at week follow up. a partial least squares discriminant analysis score scatter plot pls da score scatter plot of peripheral blood mononuclear cells metabolites at baseline n , whole grain group at follow up n , and control group at follow up n . b pls da score scatter plot of peripheral blood mononuclear cells metabolites for whole grain group at follow up n and control group at follow up n . c pls da pls da score scatter plot of plasma metabolites at baseline n , whole grain group at follow up n , and control group at follow up n . d pls da score scatter plot of plasma metabolites for whole grain group at follow up n and control group at follow up n the plasma metabolite pls da score scatter plot were not as clearly clustered as those for peripheral blood mononuclear cells metabolites r x . , r y . , q y . . for control and whole grain groups at follow up, the plasma metabolite pls da score scatter plot were not as clearly clustered as those for peripheral blood mononuclear cells metabolites r x . , r y . , q y . . to identify metabolites that differentially determined data at baseline and follow up, s plots of p and p were generated using centroid scaling. the s plots revealed that metabolites with higher or lower p values more clearly discriminated between the two groups. identification of peripheral blood mononuclear cells metabolites of , peripheral blood mononuclear cells metabolites, those that correlated with separation between the groups were identified by the variable important in the projection parameter variable important in the projection values . were highly relevant for group differences. metabolites had variable important in the projection . of these were previously identified and were unknown. those peripheral blood mononuclear cells metabolites at baseline and follow up are shown in table . there were no significant differences in baseline metabolites between two groups. after follow up, the control group showed significant changes in six peripheral blood mononuclear cells metabolite levels, whereas the whole grain group showed significant changes in seven peripheral blood mononuclear cells metabolite levels . mean sem. q . , q . , q . derived from paired t test. q . , q . , q . derived from independent t test in follow up. q . , q . , q . derived from changed values between control and whole grain groups we compared peripheral blood mononuclear cells metabolite changes between two groups. the whole grain group had greater reductions in l leucine q . , oleamide q . , lysopc q . , and lysopc q . . at follow up, the whole grain group had higher peak intensities of l pyroglutamic acid and ribothymidine, and lower peak intensities of palmitic amide, oleamide, and lysopcs, compared with those of the control group . identification of plasma metabolites of , plasma metabolites, those that correlated with separation between the groups were selected by variable important in the projection . . plasma metabolites were selected were previously identified and were unknown . there were no significant differences in baseline between two groups. after follow up, c sphinganine significantly increased in the control group, also, there were no significant differences in metabolites between two groups, and no significant differences in metabolite changes with respect to baseline . mean sem. q . , q . , q . derived from paired t test. q . , q . , q . derived from independent t test in follow up. q . , q . , q . derived from changed values between control and whole grain groups. pcs were detected by orbitrap mass spectrometer therefore, all detected pc amounts were combined. sm, sphingomyelin correlations among fasting glucose, plasma and peripheral blood mononuclear cells lp pla activities, biochemical parameters, and major peripheral blood mononuclear cells metabolites the correlation matrix of changes in glucose, lp pla activities in plasma and peripheral blood mononuclear cells , biochemical parameters, and major peripheral blood mononuclear cells metabolites was computed . analysis of metabolic changes including all subjects identified the following correlations glucose correlated positively with insulin, homeostasis model assessment insulin resistance , plasma lp pla activity r . , p . , malondialdehyde , ox low density lipoprotein , lp pla in peripheral blood mononuclear cells r . , p . , glucose auc, c peptide, hba c, and peripheral blood mononuclear cells lysopcs after adjusting for age, gender, bmi, smoking, and drinking. after adjusting for confounding variables, plasma lp pla activity correlated positively with glucose, homeostasis model assessment insulin resistance , ox low density lipoprotein , lp pla activity in peripheral blood mononuclear cells r . , p . , glucose auc, peripheral blood mononuclear cells palmitic amide, and peripheral blood mononuclear cells oleamide. after adjusting for confounding variables, peripheral blood mononuclear cells lp pla activity correlated positively with glucose, homeostasis model assessment insulin resistance , plasma lp pla activity, ox low density lipoprotein , peripheral blood mononuclear cells l leucine, peripheral blood mononuclear cells oleamide, peripheral blood mononuclear cells lysopcs, and correlated negatively with low density lipoprotein particle size . fig. correlation matrix for changes in biochemical characteristics and peripheral blood mononuclear cells metabolites in total subjects. supervised hierarchical clustering identifies the most important metabolites and biochemical characteristics. correlations were obtained by deriving spearman correlation coefficients. red, positive correlation. purple, negative correlation discussion we identified four peripheral blood mononuclear cells metabolites that had statistically significant differences after dietary intervention, including l leucine, oleamide, lysopc , and lysopc however, there were no significant differences in plasma metabolites after dietary intervention. these aspects of results were also shown in both subjects with prediabetes and type diabetes , respectively. peripheral blood mononuclear cells s may be a useful tool for nutrigenomics and understanding the pathophysiology of chronic disease due to their active metabolism , . these results identify peripheral blood mononuclear cells metabolites as powerful metabolomics tools to detect diet induced metabolic changes. improving glycemic control in the whole grain group decreases ox low density lipoprotein , and reduces peripheral blood mononuclear cells lp pla activity and peripheral blood mononuclear cells lysopcs. a strong correlation between peripheral blood mononuclear cells lp pla activity and ox low density lipoprotein , but not low density lipoprotein cholesterol, is consistent with a previous report of a direct effect of ox low density lipoprotein on lp pla expression in thp monocytes . ox low density lipoprotein may upregulate peripheral blood mononuclear cells lp pla expression in smokers . ox phospholipids in low density lipoprotein particles are hydrolyzed by lp pla at the sn position to produce bioactive ox free fatty acids s and lysopcs. only of the total non ox low density lipoprotein pc content is lysopc however, up to of low density lipoprotein pc is converted to lysopc during low density lipoprotein oxidation . this study identified strongly positive correlations among ox low density lipoprotein , peripheral blood mononuclear cells lp pla activity, peripheral blood mononuclear cells lysopcs, which may indicate that ox low density lipoprotein and peripheral blood mononuclear cells lp pla activity are major determinants of peripheral blood mononuclear cells lysopc levels. a negative correlation between peripheral blood mononuclear cells lp pla activities, peripheral blood mononuclear cells lysopcs with low density lipoprotein particle size is consistent with a previous report of lp pla binding preference for small dense low density lipoprotein . this study and other work reported positive correlations among glucose, peripheral blood mononuclear cells lp pla activity, and plasma lp pla activity. a strongly positive correlation between peripheral blood mononuclear cells and plasma lp pla activities also is observed in healthy subjects , . in a porcine diabetes model, peripheral blood mononuclear cells lp pla expression is upregulated in the presence of glycation end products . increases in circulating lp pla activity and increased ox low density lipoprotein levels in hypercholesterolemic pigs are primarily due to plaque macrophages . these results indicate that the primary sources of plasma lp pla are plaque macrophages and peripheral blood mononuclear cells . this could explain our observations of lower plasma lp pla activity changes compared with that of peripheral blood mononuclear cells lp pla activity, and no significant differences in plasma metabolite changes between two groups. reduced lp pla activity in plasma and peripheral blood mononuclear cells in the whole grain group could be a marker of metabolic changes induced by increased consumption of protein relative to carbohydrate. diet composition is an important factor in inflammatory processes of blood cells . a study of macronutrient composition determined that increasing dietary protein from energy intake to yielded immediate and persistent downregulation of immunological genes in peripheral blood mononuclear cells s . replacing of energy from carbohydrates with energy from protein and measured a . nmol min ml reduction in lp pla activity that was independent of other changes in lipid profiles . our study replaced of energy from carbohydrate with approximately energy from protein and energy from fat. whole grains, legumes, and vegetables contain many antioxidants, vitamins, minerals, and phytochemicals , . antioxidants slow the oxidation rate of reduced substrates , . soybean phytochemicals reduce lipid peroxidation in vivo and attenuate low density lipoprotein oxidation . our observed changes in glucose and homeostasis model assessment insulin resistance strongly correlated with changes in malondialdehyde and ox low density lipoprotein in patients with prediabetes or type diabetes , consistent with a previous report . we observed positive correlation between changes in homeostasis model assessment insulin resistance and peripheral blood mononuclear cells l leucine, but not plasma l leucine. this may be due to a negligible effect of peripheral blood mononuclear cells l leucine on plasma l leucine, or the week dietary intervention may not be long enough to change plasma l leucine. the whole grain group also had greater reduction in peripheral blood mononuclear cells oleamide, but not in plasma, compared with control group. we identified peripheral blood mononuclear cells oleamide variable important in the projection . as the most important metabolite for evaluating differences between two groups at the end of the study. recently, ha et al. identified plasma oleamide as the most important metabolite for distinguishing nondiabetic from diabetic males. therefore, positive correlations between changes in peripheral blood mononuclear cells oleamide, lp pla , peripheral blood mononuclear cells palmitic amide, and peripheral blood mononuclear cells lysopcs observed in our study could be partly due to dietary induced effects on blood cell inflammatory processes . this study detected many metabolic markers using uplc ltq orbitrap mass spectrometer , but most are currently unidentified. endogenous biomolecule databases for use with lc mass spectrometer based metabolomics research are still under construction . despite this limitation, uplc ltq orbitrap mass spectrometer metabolomics and multivariate data analysis identified greater reductions in peripheral blood mononuclear cells l leucine, peripheral blood mononuclear cells oleamide, peripheral blood mononuclear cells lysopcs in the whole grain group than control group however, there were no significant differences in plasma metabolites between two groups. conclusion this study demonstrates that replacing refined rice with whole grains and legumes induced greater differences in peripheral blood mononuclear cells lp pla activity and metabolites than in plasma metabolites in nonobese patients with prediabetes or newly diagnosed type diabetes . therefore, consumption of minimally refined grains, legumes, and vegetables should be recommended to control glucose metabolism and reduce cardiovascular risk factors in patients with impaired fasting glucose , impaired glucose tolerance , or newly diagnosed type diabetes . abbreviations lp pla lipoprotein associated phospholipase a type diabetes type diabetes peripheral blood mononuclear cells peripheral blood mononuclear cell impaired fasting glucose impaired fasting glucose impaired glucose tolerance impaired glucose tolerance bmi body mass index blood pressure blood pressure high density lipoprotein high density lipoprotein low density lipoprotein low density lipoprotein free fatty acids free fatty acid hba c hemoglobin a c insulin resistance insulin resistance homeostasis model assessment homeostasis model assessment fetal bovine serum fetal bovine serum hs crp high sensitivity creactive protein malondialdehyde malondialdehyde thiobarbituric acid reactive substances thiobarbituric acid reactive substances ox oxidized mass spectrometer mass spectrometer pls da partial leastsquares discriminant analysis waist hip ratio waist hip ratio auc area under the curve variable important in the projection variable important in the projection. competing interests the authors declare that they have no competing interests. authors' contributions all the authors were involved in the development of the study protocol and the experimental design. gs, mk and jhy collected samples and carried out experiments. mk performed data analysis. t sj, s hl and jhl reviewed data and participated in general discussion. jhl provided the research funding and wrote the manuscript. all the authors read, commented on, and contributed to the submitted manuscript. all authors read and approved the final manuscript. acknowledgments this research was supported by the bio synergy research projects national research foundation m a c of the national research foundation funded by the ministry of science, ict future planning, republic of korea. author details research center for silver science, institute of symbiotic life tech, yonsei university, seoul , republic of korea. national leading research laboratory of clinical nutrigenetics nutrigenomics, department of food and nutrition, college of human ecology, yonsei university, seoul , republic of korea. department of food and nutrition, brain korea plus project, college of human ecology, yonsei university, yonsei ro, seodaemun gu, seoul , republic of korea. national research laboratory of lipid metabolism and atherosclerosis, korea research institute of bioscience and biotechnology, daejeon , republic of korea. department of family practice, national health insurance corporation ilsan hospital, goyang , republic of korea. received october accepted january

answer

peripheral blood mononuclear cells

[tomhosking]

Weird - it works fine on my local instance of the demo. The version running online is a bit out of date, so perhaps has some bug that gets triggered by long documents. The current version in the repo seems to work though, so I suggest you run that.

[SundeepPidugu]

@tomhosking Thanks