Miracle-dz/UniFAR-FTUs huggingface dataset:
Production rate of acetate during colonic fermentation of lactulose: a stable-isotope study in humans.

BACKGROUND Breath tests are currently used to qualitatively assess colonic fermentation; no quantitative estimations are available for healthy subjects. OBJECTIVE This study describes a stable-isotope-dilution method to measure acetate production quantitatively from colonic bacterial fermentation. DESIGN Six volunteers received a primed, constant, intravenous infusion of [1-13C]acetate at a rate of 1.01 +/- 0.04 micromol x kg(-1) x min(-1) for 7 h. They ingested 20 g pure lactulose after 1 h of the tracer infusion. Expired air and arterialized venous blood were sampled every 15 min. RESULTS Before lactulose intake, the breath-hydrogen concentration was 7 +/- 2 ppm and the plasma acetate concentration and isotopic enrichment were 141 +/- 14 micromol/L and 14.8 +/- 1.4 moles percent excess, respectively. Whole-body acetate turnover was 6.0 +/- 0.7 micromol x kg(-1) x min(-1). After lactulose ingestion, maximum breath hydrogen and acetate concentrations reached 63 +/- 15 ppm (P = 0.004) and 313 +/- 25 micromol/L (P = 0.002), respectively, whereas [13C]acetate enrichment decreased to 9.9 +/- 1.3 moles percent excess (P = 0.03). Whole-body acetate turnover increased to 9.8 +/- 1.5 micromol x kg(-1) x min(-1) and later decreased almost to baseline values. Colonic lactulose fermentation yielded 140 +/- 12 mmol acetate over 6 h, representing 86% of the production based on stoichiometric equations. CONCLUSION This new method provides a quantitative estimate of colonic carbohydrate fermentation via evaluation of acetate production.
Nutritional and health consequences are associated with food insecurity among U.S. elderly persons.

The purpose of this study was to examine the consequences associated with food insecurity for the nutritional and health status of the elderly in the United STATES: The data analyzed were from the Third National Health and Nutrition Examination Survey (1988-1994) and the Nutrition Survey of the Elderly in New York State (1994). Multiple logistic and linear regression analyses were used to assess the extent to which food-insecure elderly were likely to have lower nutrient intake, skinfold thickness, self-reported health status and higher nutritional risk. Regardless of food insecurity status, older people consumed less than the recommended dietary allowance for eight nutrients. Food-insecure elderly persons had significantly lower intakes of energy, protein, carbohydrate, saturated fat, niacin, riboflavin, vitamins B-6 and B-12, magnesium, iron and zinc, as well as lower skinfold thickness. In addition, food-insecure elderly persons were 2.33 (95% confidence interval: 1.73-3.14) times more likely to report fair/poor health status and had higher nutritional risk. These results indicate that food-insecure elderly persons have poorer dietary intake, nutritional status and health status than do food-secure elderly persons. It is necessary to ensure the nutritional well-being of all elderly persons who are at nutritional and health risk, including those who are food insecure and have even poorer nutritional and health status than those who are food secure.
Poor micronutrient status of active pulmonary tuberculosis patients in Indonesia.

Malnutrition is observed frequently in patients with pulmonary tuberculosis (TB), but their nutritional status, especially of micronutrients, is still poorly documented. The objective of this study was to investigate the nutritional status of patients with active TB compared with that of healthy controls in Jakarta, Indonesia. In a case-control study, 41 out-patients aged 15-55 y with untreated active pulmonary TB were compared with 41 healthy controls selected from neighbors of the patients and matched for age and sex. Cases had clinical and radiographic abnormalities consistent with pulmonary TB and at least two sputum specimens showing acid-fast bacilli. Anthropometric and micronutrient status data were collected. Compared with the controls, TB patients had significantly lower body mass index, skinfold thicknesses (triceps, biceps, subscapular, suprailiac), mid-upper arm circumference, proportion of fat, and concentrations of serum albumin, blood hemoglobin, plasma retinol and plasma zinc, whereas plasma zinc protoporphyrin concentration, as a measure of free erythrocyte protoporphyrin concentration, was greater. When patients and controls were subdivided on the basis of nutritional status, concentrations of serum albumin, blood hemoglobin, and zinc and retinol in plasma were lower in malnourished TB patients than in well-nourished healthy controls, well-nourished TB patients and malnourished healthy controls. In conclusion, the nutritional status of patients with active pulmonary TB was poor compared with healthy subjects, i.e., significantly more patients were anemic and more had low plasma concentrations of retinol and zinc. Low concentrations of hemoglobin, and of retinol and zinc in plasma were more pronounced in malnourished TB patients.
One low-dose exposure of gold nanoparticles induces long-term changes in human cells

Significance Gold nanoparticles are promising candidates for optical sensing, bioimaging, delivery, and therapeutic applications due to their size- and shape-dependent physical properties and inherent biocompatibility compared with other metallic nanoparticles. Many studies have found that these particles are generally nontoxic at low doses for most, but not all, initial surface treatments. In this study, a long-term (20 wk) exposure of a set of gold nanoparticles to a human cell line was performed in two ways: an acute burst of nanoparticle exposure compared with a continuous, chronic exposure at the same concentration. Overall, it was found that an acute burst of exposure is more harmful to cells, and that cells can adapt to long-term nanoparticle exposure. We report the in vitro long-term (20 wk) changes in cells exposed to well-characterized gold nanoparticles (Au NPs) with varying shapes and surface coatings under both chronic (exposure to Au NPs continuously over 20 wk) and nonchronic (initial acute cell exposure to Au NPs, followed by 20 wk in NP-free cell media) conditions. Both chronic and nonchronic Au NPs exposures at low dose induce modifications at the gene level after long periods. In attempt to overcome from the injuries caused by nanoparticle exposure, genes related to oxidative stress, cell cycle regulation, and inflammation are among those presenting differential expression levels. Surprisingly, the nonchronic exposure induced more gene expression changes than its chronic counterpart and the stress effects caused by this type of exposure were sustained even after 20 wk without any additional NP exposure. NP surface chemistry played an important role in the alteration of gene regulation. Overall, our data suggest that (i) cells can adaptively respond to chronic, low-level NP insults; (ii) the cell stress response is not reversible over time upon removal of NPs upon acute, nonchronic exposure; and (iii) polyethylene glycol is not as benign a surface chemistry as is generally supposed.
Polymorphisms of methylenetetrahydrofolate reductase and other enzymes: metabolic significance, risks and impact on folate requirement.

A common genetic polymorphism results from a C-->T substitution in the gene encoding methylenetetrahydrofolate reductase (MTHFR), the enzyme that produces 5-methyltetrahydrofolate (5-methyl-THF) required for the conversion of homocysteine to methionine. In individuals with the T/T genotype (T/T), functional metabolic effects include changes in one-carbon folate derivatives, elevations in plasma homocysteine and differences in response to folic acid supplementation compared with normal (C/C) or heterozygous (C/T) genotypes. The metabolic changes associated with the T/T genotype are postulated to modify risk for chronic disease (e.g., vascular disease and cancer) and neural tube defects (NTD) when accompanied by folate deficiency. The modulation of these metabolic abnormalities by increasing folate intake suggests that folate requirements may be different in affected individuals (T/T) relative to normal (C/C) or heterozygous (C/T) individuals. The complex interaction between this common genetic polymorphism of MTHFR and folate intake is the focus of intense investigation.
A Heterogeneous Network Based Method for Identifying GBM-Related Genes by Integrating Multi-Dimensional Data

The emergence of multi-dimensional data offers opportunities for more comprehensive analysis of the molecular characteristics of human diseases and therefore improving diagnosis, treatment, and prevention. In this study, we proposed a heterogeneous network based method by integrating multi-dimensional data (HNMD) to identify GBM-related genes. The novelty of the method lies in that the multi-dimensional data of GBM from TCGA dataset that provide comprehensive information of genes, are combined with protein-protein interactions to construct a weighted heterogeneous network, which reflects both the general and disease-specific relationships between genes. In addition, a propagation algorithm with resistance is introduced to precisely score and rank GBM-related genes. The results of comprehensive performance evaluation show that the proposed method significantly outperforms the network based methods with single-dimensional data and other existing approaches. Subsequent analysis of the top ranked genes suggests they may be functionally implicated in GBM, which further corroborates the superiority of the proposed method. The source code and the results of HNMD can be downloaded from the following URL: http://bioinformatics.ustc. edu.cn/hnmd/ .
Aquaporin-3 mediates hydrogen peroxide-dependent responses to environmental stress in colonic epithelia

Significance The extracellular production of hydrogen peroxide (H2O2) by membrane or secreted oxidases has been linked to epithelial wound repair, defense against infection, and inflammation. Here, we elucidate the pathway that explains how extracellular H2O2 transduces a signal into the cell to induce these critical cell functions. Our study shows the central component of this pathway in the mammalian colon is the H2O2-conducting aquaglyceroporin AQP3 and implicates this channel in innate immune responses at mucosal surfaces. The colonic epithelium provides an essential barrier against the environment that is critical for protecting the body and controlling inflammation. In response to injury or gut microbes, colonic epithelial cells produce extracellular hydrogen peroxide (H2O2), which acts as a potent signaling molecule affecting barrier function and host defense. In humans, impaired regulation of H2O2 in the intestine has been associated with early-onset inflammatory bowel disease and colon cancer. Here, we show that signal transduction by H2O2 depends on entry into the cell by transit through aquaporin-3 (AQP3), a plasma membrane H2O2-conducting channel. In response to injury, AQP3-depleted colonic epithelial cells showed defective lamellipodia, focal adhesions, and repair after wounding, along with impaired H2O2 responses after exposure to the intestinal pathogen Citrobacter rodentium. Correspondingly, AQP3−/− mice showed impaired healing of superficial wounds in the colon and impaired mucosal innate immune responses against C. rodentium infection, manifested by reduced crypt hyperplasia, reduced epithelial expression of IL-6 and TNF-α, and impaired bacterial clearance. These results elucidate the signaling mechanism of extracellular H2O2 in the colonic epithelium and implicate AQP3 in innate immunity at mucosal surfaces.
Zinc absorption as a function of the dose of zinc sulfate in aqueous solution.

BACKGROUND Zinc supplements are used extensively in medicine and research and for public health purposes in the prevention and treatment of zinc deficiency. However, little is known about the efficiency of zinc utilization after different doses. OBJECTIVE The objective was to determine the relation between dose of aqueous zinc and absorbed zinc (AZ) in healthy adults. DESIGN Eight healthy adults (3 men and 5 women) aged 33.8 +/- 9.8 y (x +/- SD) received 3 pairs of zinc doses (2 and 5, 10 and 15, and 20 and 30 mg) in random order in 3 phases (1 pair per phase). There was a 3-wk washout between phases. Aqueous zinc sulfate labeled with 70Zn or 68Zn was orally administered in the postabsorptive state on days 1 and 6, respectively; intravenous 67Zn was administered 1 h after the first oral zinc dose. Two urine samples were collected daily from days 3 to 15; zinc isotopic ratios were determined by inductively coupled plasma mass spectrometry. Fractional absorption of zinc (FAZ) was determined by dual-isotope-tracer ratio; AZ was calculated by multiplying FAZ by dose. RESULTS Mean (+/-SD) AZ values at doses of 2.2, 5.2, 10.4, 15.2, 20.3, and 30.1 mg ingested Zn were 1.6 +/- 0.4, 3.5 +/- 1.3, 7.4 +/- 1.0, 9.5 +/- 2.2, 11.0 +/- 4.4, and 11.2 +/- 2.1 mg, respectively. A saturable dose-response model, the Hill equation, was selected to model the relation of AZ to ingested zinc. Parameter estimation by nonlinear regression predicted a maximum zinc absorption of 13 mg for larger doses. CONCLUSIONS Increases in aqueous zinc doses >20 mg result in relatively small and progressively diminishing increases in AZ postabsorptively in healthy adults.
Reactive local navigation

In this paper a reactive local navigation system is presented, for an autonomous nonholonomic mobile robot navigating in dynamic environments. The reactive navigation system integrates an obstacle detection method and a new reactive collision avoidance method. The sensory perception is based in a laser range finder (LRF) system. Simulation results are presented to verify the effectiveness of the proposed local navigation system in unknown environments with multiple moving objects. The comparison of results are shown, between two different approaches, a velocity obstacle (VO) approach and our own, based in the dynamic window (DW) concept.
Effects of purified eicosapentaenoic and docosahexaenoic acids on glycemic control, blood pressure, and serum lipids in type 2 diabetic patients with treated hypertension.

BACKGROUND n-3 Fatty acids lower blood pressure, improve lipids, and benefit other cardiovascular disease risk factors. Effects on glycemia in patients with type 2 diabetes are uncertain. OBJECTIVE We determined whether purified eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have differential effects on glycemic control, including insulin sensitivity and stimulated insulin secretion; 24-h ambulatory blood pressure; and serum lipids in type 2 diabetic patients with treated hypertension. DESIGN In a double-blind, placebo-controlled trial of parallel design, 59 subjects were randomly assigned to consume 4 g EPA, DHA, or olive oil/d for 6 wk while continuing to consume their usual diet. RESULTS Thirty-nine men and 12 postmenopausal women with a mean (+/- SE) age of 61.2 +/- 1.2 y completed the study. In comparison with the change from baseline in fasting glucose in the olive oil group, fasting glucose in the EPA and DHA groups increased 1.40 +/- 0.29 mmol/L (P = 0.002) and 0.98 +/- 0.29 mmol/L (P = 0.002), respectively. Neither EPA nor DHA had significant effects on glycated hemoglobin, fasting insulin or C-peptide, insulin sensitivity or secretion, or blood pressure. Serum triacylglycerols in the EPA and DHA groups decreased 19% (P = 0.022) and 15% (P = 0.022), respectively. There were no significant changes in serum total, LDL, or HDL cholesterol, although HDL(2) cholesterol in the EPA and DHA groups increased 16% (P = 0.026) and 12% (P = 0.05), respectively. HDL(3) cholesterol decreased 11% (P = 0.026) with EPA supplementation. CONCLUSIONS EPA and DHA had similar benefits on lipids but adverse effects on short-term glycemic control in hypertensive diabetic patients. The overall implications for cardiovascular disease require long-term evaluation.
Effects of age of introduction of complementary foods on iron status of breast-fed infants in Honduras.

To evaluate the effect of introducing complementary foods before 6 mo of age, we randomly assigned 164 infants who had been exclusively breast-fed for 4 mo to continue being exclusively breast-fed until 6 mo (EBF group) or to receive iron-fortified foods in addition to breast milk from 4 to 6 mo (BF+SF group). At 6 mo, the BF+SF group had higher mean iron intake (4 mg/d compared with 0.2 mg/d in EBF infants) and higher hemoglobin, hematocrit, and ferritin values than the EBF group (P < 0.05). The percentage with low hemoglobin (< 103 g/L) did not differ significantly between groups, but fewer infants in the BF+SF group had a low hematocrit (< 0.33; 21.4% compared with 32.0%, respectively; P < 0.05). The percentage of infants with ferritin concentrations < 12 microg/L at 6 mo was lower than the percentage with low hemoglobin or hematocrit, raising questions about the validity of the cutoffs at this age. Infants at greatest risk for anemia and low ferritin were those with birth weights < 2500 g; no infant with a birth weight > 3000 g had a low ferritin value at 6 mo. We conclude that the risk of iron deficiency is low among infants with birth weights > 3000 g who are exclusively breast-fed for 6 mo. Iron drops are recommended for low-birth-weight infants; for breast-fed infants with birth weights between 2500 and 3000 g, further research is needed to determine whether iron drops are more effective than complementary foods for preventing iron deficiency before 6 mo.
Plasma lipids and lipoproteins in hypercholesterolemic men fed a lipid-lowering diet containing lean beef, lean fish, or poultry.

BACKGROUND To reach desirable lipid and lipoprotein concentrations, patients with hypercholesterolemia are often told to replace the consumption of beef with that of fish and poultry. OBJECTIVE The objective of this study was to compare the effects on lipoprotein profiles in hypercholesterolemic men of the incorporation of lean beef, poultry (without skin), and lean fish into an American Heart Association diet with a high polyunsaturated-to-saturated fatty acid ratio and a high fiber content. DESIGN Three groups of subjects each rotated in a crossover design through 3 experimental periods that lasted 26 d each. The diets were planned to provide 11 713 kJ/d, of which 18% came from protein, 53% from carbohydrate, and 30% from lipids (polyunsaturated-to-monounsaturated-to-saturated fatty acid ratio: 1.0:1.1:1.0); 268 mg cholesterol/d; and 29 g fiber/d. RESULTS The lean beef, lean fish, and poultry diets reduced plasma total and LDL cholesterol by 5-9%, LDL apolipoprotein B by 16-19%, VLDL triacylglycerols by 22-31%, and the ratio of total cholesterol to HDL cholesterol by 6-11%; they also increased the ratio of LDL cholesterol to apolipoprotein B by 18-28%. No significant difference was found in these lipid variables between the 3 experimental diets. However, the lean fish diet increased HDL(2) cholesterol significantly more (P < 0.05) than did the lean beef diet and the ratio of HDL(2) to HDL(3) cholesterol significantly more (P < 0.05) than did the lean beef and poultry diets. CONCLUSION The results indicate that an American Heart Association diet with a high polyunsaturated-to-saturated fatty acid ratio and high fiber content induced numerous favorable changes in coronary artery disease risk factors in hypercholesterolemic men, regardless of the protein source.
The effects of high and low doses of folic acid on oxidation of protein levels during pregnancy: a randomized double-blind clinical trial

Abstract Objective Oxidants include important active molecules which are created in the body and attack biological molecules especially lipids, carbohydrates, nucleic acids and proteins, and cause oxidation and various diseases in the body. Antioxidants existing in the body help to avoid the incidence of these injuries. Pregnant women are among those where oxidation of biological molecules may do irreparable damage to them and their embryos. So, the purpose of this study was to review the effect of folic acid with both high (5 mg/day) and low (0.5 mg/day) doses on the changes of oxidative protein in reducing plasma homocystein concentration during pregnancy. Materials and methods Forty-five pregnant women participated in this study. They were divided into two groups: group 1 included 23 women who received 5 mg/day folic acid and group 2 included 23 women who took 0.5 mg/day folic acid before pregnancy till the 36th week pregnancy. We measured the biochemical variables in the serum of pregnant women at the beginning and at the end of the study. Results Folic acid reduced plasma homocytein in both low and high dose groups (p = 0.035, p = 0.012, respectively). Also, the results showed that folic acid prescription led to reduce plasma level of carbonyl groups in both low and high dose groups (p = 0.01, p = 0.03, respectively). Furthermore, the results showed that there is no significant difference between two groups and folic acid affects both groups equally. Conclusion It is possible that folic acid administration can reduce plasma homocysteine and carbonyl levels during pregnancy in dose independent manner
The urgent need to recommend an intake of vitamin D that is effective.

This editorial makes the point that there is now strong evidence that increasing vitamin D intake will lower risk of falling and lower fracture risk in older men and women. There is also strong evidence that higher vitamin D intakes are safe. Currently recommended intakes of vitamin D are insufficient to minimize risk of falling and risk of fracture. The authors of this editorial urge regulatory agencies in the United States and abroad to review the evidence and reassess their dietary recommendations for vitamin D.
Differential methylation tests of regulatory regions

Abstract Differential methylation of regulatory elements is critical in epigenetic researches and can be statistically tested. We developed a new statistical test, the generalized integrated functional test (GIFT), that tests for regional differences in methylation based on the methylation percent at each CpG site within a genomic region. The GIFT uses estimated subject-specific profiles with smoothing methods, specifically wavelet smoothing, and calculates an ANOVA-like test to compare the average profile of groups. In this way, possibly correlated CpG sites within the regulatory region are compared all together. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing methods can be used to estimate the profiles of data without noise. Matlab code for GIFT and sample data are available at http://www.augusta. edu/mcg/biostatepi/people/software/gift.html.
Structural zeros in high‐dimensional data with applications to microbiome studies

&NA; This paper is motivated by the recent interest in the analysis of high‐dimensional microbiome data. A key feature of these data is the presence of “structural zeros” which are microbes missing from an observation vector due to an underlying biological process and not due to error in measurement. Typical notions of missingness are unable to model these structural zeros. We define a general framework which allows for structural zeros in the model and propose methods of estimating sparse high‐dimensional covariance and precision matrices under this setup. We establish error bounds in the spectral and Frobenius norms for the proposed estimators and empirically verify them with a simulation study. The proposed methodology is illustrated by applying it to the global gut microbiome data of Yatsunenko and others (2012. Human gut microbiome viewed across age and geography. Nature 486, 222–227). Using our methodology we classify subjects according to the geographical location on the basis of their gut microbiome.