Miracle-dz/UniFAR-FTUs huggingface dataset:
Rational Design of Cyclic Antimicrobial Peptides Based on BPC194 and BPC198

A strategy for the design of antimicrobial cyclic peptides derived from the lead compounds c(KKLKKFKKLQ) (BPC194) and c(KLKKKFKKLQ) (BPC198) is reported. First, the secondary β-structure of BPC194 and BPC198 was analyzed by carrying out molecular dynamics (MD) simulations. Then, based on the sequence pattern and the β-structure of BPC194 or BPC198, fifteen analogues were designed and synthesized on solid-phase. The best peptides (BPC490, BPC918, and BPC924) showed minimum inhibitory concentration (MIC) values <6.2 μM against Pseudomonas syringae pv. syringae and Xanthomonas axonopodis pv. vesicatoria, and an MIC value of 12.5 to 25 μM against Erwinia amylovora, being as active as BPC194 and BPC198. Interestingly, these three analogues followed the structural pattern defined from the MD simulations of the parent peptides. Thus, BPC490 maintained the parallel alignment of the hydrophilic pairs K1–K8, K2–K7, and K4–K5, whereas BPC918 and BPC924 included the two hydrophilic interactions K3–Q10 and K5–K8. In short, MD simulations have proved to be very useful for ascertaining the structural features of cyclic peptides that are crucial for their biological activity. Such approaches could be further employed for the development of new antibacterial cyclic peptides.
Carbohydrate ingestion can completely suppress endogenous glucose production during exercise.

The purposes of this study were 1) to investigate the effect of carbohydrate (CHO) ingestion on endogenous glucose production (EGP) during prolonged exercise, 2) to study whether glucose appearance in the circulation could be a limiting factor for exogenous CHO oxidation, and 3) to investigate whether large CHO feedings can reduce muscle glycogen oxidation during exercise. Six well-trained subjects exercised three times for 120 min at 50% maximum workload while ingesting water (FAST), a 4% glucose solution (LO-Glc), or a 22% glucose solution (HI-Glc). A primed continuous intravenous [6,6-2H2]glucose infusion was given, and the ingested glucose was enriched with [U-13C]glucose. Glucose ingestion significantly elevated CHO oxidation as well as the rates of appearance (Ra) and disappearance. Ra glucose equaled Ra of glucose in gut (Ra gut) during HI-Glc, whereas EGP was completely suppressed. During LO-Glc, EGP was partially suppressed, whereas Ra gut provided most of the total glucose Ra. We conclude that 1) high rates of CHO ingestion can completely block EGP, 2) Ra gut may be a limiting factor for exogenous CHO oxidation, and 3) muscle glycogen oxidation was not reduced by large glucose feedings.
Recent Advances in Conotoxin Classification by Using Machine Learning Methods

Conotoxins are disulfide-rich small peptides, which are invaluable peptides that target ion channel and neuronal receptors. Conotoxins have been demonstrated as potent pharmaceuticals in the treatment of a series of diseases, such as Alzheimer’s disease, Parkinson’s disease, and epilepsy. In addition, conotoxins are also ideal molecular templates for the development of new drug lead compounds and play important roles in neurobiological research as well. Thus, the accurate identification of conotoxin types will provide key clues for the biological research and clinical medicine. Generally, conotoxin types are confirmed when their sequence, structure, and function are experimentally validated. However, it is time-consuming and costly to acquire the structure and function information by using biochemical experiments. Therefore, it is important to develop computational tools for efficiently and effectively recognizing conotoxin types based on sequence information. In this work, we reviewed the current progress in computational identification of conotoxins in the following aspects: (i) construction of benchmark dataset; (ii) strategies for extracting sequence features; (iii) feature selection techniques; (iv) machine learning methods for classifying conotoxins; (v) the results obtained by these methods and the published tools; and (vi) future perspectives on conotoxin classification. The paper provides the basis for in-depth study of conotoxins and drug therapy research.
Localization of the extracellular Ca2+/polyvalent cation-sensing protein in rat kidney.

We previously identified transcripts encoding a G protein-coupled, extracellular calcium/polyvalent cation-sensing receptor, RaKCaR, in rat kidney (D. Riccardi, J. Park, W.-S. Lee, G. Gamba, E. M. Brown, and S. C. Hebert. Proc. Natl. Acad. Sci. USA 92: 131-135, 1994), which was proposed to provide the mechanism for modulating a variety of renal functions in response to changes in extracellular Ca2+ (E. M. Brown. In: Handbook of Physiology. Bethesda, MD: Am. Physiol. Soc., 1992, sect. 8, vol. 2, chapt. 39, p. 1841-1916; and S. C. Hebert. Kidney Int. 50: 2129-2139, 1996). Here, we examine the cellular and regional distribution of receptor protein by immunofluorescence microscopy using a polyclonal antibody raised against a 22 amino acid region of the NH2 terminus of the receptor. The most intense fluorescence was seen at the basolateral border of cortical thick ascending limb cells. Basolateral staining for the receptor was also detected in medullary thick ascending limbs, in macula densa cells identified by costaining with antibody to brain nitric oxide synthase, NOS-B1, and in distal convoluted tubule cells distinguished by costaining for the apical thiazide-sensitive Na+-Cl-cotransporter. Apical anti-RaKCaR staining was detected at the base of the brush border of proximal tubules with decreasing intensity from S1 to S3 segments. In cortical collecting ducts, anti-RaKCaR staining was detected in some, but not all, type A intercalated cells identified by costaining with anti-H+-ATPase and anti-AE1 Cl-/[Formula: see text]exchanger antibodies. The present study demonstrates that RaKCaR protein is expressed in many different nephron segments and that the polarity of receptor expression varies with cell type along the nephron. These results suggest potential roles for the extracellular Ca2+/polyvalent cation-sensing receptor in responding to both circulating and urinary concentrations of divalent minerals and potentially other polyvalent cations (e.g., aminoglycoside antibiotics) to modulate nephron function.
Associations between prenatal and infancy weight gain and BMI, fat mass, and fat distribution in young adulthood: a prospective cohort study in males and females born very preterm.

BACKGROUND Increasing evidence indicates that adult body composition is associated with prenatal and infancy weight gain, but the relative importance of different time periods has not been elucidated. OBJECTIVE The objective was to study the association between prenatal, early postnatal, and late infancy weight gain and body mass index (BMI), fat mass, and fat distribution in young adulthood. DESIGN We included 403 men and women aged 19 y from a Dutch national prospective follow-up study who were born at <32 wk of gestation. BMI, waist circumference, and waist-to-hip ratio SD scores and subscapular-to-triceps ratio, percentage body fat, fat mass, and fat-free mass at age 19 y were studied in relation to birth weight SD scores, weight gain from preterm birth until 3 mo postterm (early postnatal weight gain), and weight gain from 3 mo until 1 y postterm (late infancy weight gain). RESULTS Birth weight SD scores were positively associated with weight, height, BMI SD scores, and fat-free mass at age 19 y but not with fat mass, percentage body fat, or fat distribution. Early postnatal and late infancy weight gain were positively associated with adult height, weight, BMI, waist circumference SD scores, fat mass, fat-free mass, and percentage body fat but not with waist-to-hip ratio SD scores or subscapular-to-triceps ratio. CONCLUSIONS In infants born very preterm, weight gain before 32 wk of gestation is positively associated with adult body size but not with body composition and fat distribution. More early postnatal and, to a lesser extent, late infancy weight gain are associated with higher BMI SD scores and percentage body fat and more abdominal fat at age 19 y.
Flavonoid intake and cardiovascular disease mortality: a prospective study in postmenopausal women.

BACKGROUND Dietary flavonoids may have beneficial cardiovascular effects in human populations, but epidemiologic study results have not been conclusive. OBJECTIVE We used flavonoid food composition data from 3 recently available US Department of Agriculture databases to improve estimates of dietary flavonoid intake and to evaluate the association between flavonoid intake and cardiovascular disease (CVD) mortality. DESIGN Study participants were 34 489 postmenopausal women in the Iowa Women's Health Study who were free of CVD and had complete food-frequency questionnaire information at baseline. Intakes of total flavonoids and 7 subclasses were categorized into quintiles, and food sources were grouped into frequency categories. Proportional hazards rate ratios (RR) were computed for CVD, coronary heart disease (CHD), stroke, and total mortality after 16 y of follow-up. RESULTS After multivariate adjustment, significant inverse associations were observed between anthocyanidins and CHD, CVD, and total mortality [RR (95% CI) for any versus no intake: 0.88 (0.78, 0.99), 0.91 (0.83, 0.99), and 0.90 (0.86, 0.95)]; between flavanones and CHD [RR for highest quintile versus lowest: 0.78 (0.65, 0.94)]; and between flavones and total mortality [RR for highest quintile versus lowest: 0.88 (0.82, 0.96)]. No association was found between flavonoid intake and stroke mortality. Individual flavonoid-rich foods associated with significant mortality reduction included bran (added to foods; associated with stroke and CVD); apples or pears or both and red wine (associated with CHD and CVD); grapefruit (associated with CHD); strawberries (associated with CVD); and chocolate (associated with CVD). CONCLUSION Dietary intakes of flavanones, anthocyanidins, and certain foods rich in flavonoids were associated with reduced risk of death due to CHD, CVD, and all causes.
Incorporation of docosahexaenoic acid into nerve membrane phospholipids: bridging the gap between animals and cultured cells.

BACKGROUND Functional maturation of nervous tissues depends on membrane accretion of docosahexaenoic acid (DHA). Animal studies have shown that incorporation of dietary DHA into membrane phospholipids is dose dependent. The molecular effects of DHA are commonly studied in cultured cells, but questions remain about the physiologic connection between animal and cell models. OBJECTIVE We developed a linear model for comparing the responses of rat nervous tissues to dietary DHA with the responses of human cell lines to DHA in medium. DESIGN Rats were rendered chronically deficient in n-3 fatty acids by being reared on a peanut oil diet. DHA status was replenished in the F2 generation by using increasing supplements of a microalgal oil. Human retinoblastoma and neuroblastoma cells were dosed with unesterified DHA. DHA accumulation into phospholipids was defined by the plateau of the dose-response curve (DHA(max)) and by the supplement required to produce one-half the DHA(max) (DHA(50)). RESULTS The DHA(max) values for 4 brain regions and 2 neuroblastoma lines were similar, and the value for the retinoblastoma line was similar to the retinal value. Expressing the DHA input as micro mol/10 g diet and as micro mol/L medium resulted in similar values for the ratio of DHA(max) to DHA(50) in the 4 brain regions and the 3 cell lines. The DHA(max)-DHA(50) ratios in the ethanolamine phosphoglyceride and phosphatidylcholine fractions in retinal phospholipids were 6 and 10 times, respectively, those in the brain and cultured cells. CONCLUSIONS The dose-dependent responses of cells and the brain to DHA supplements can be compared by using DHA(max)-DHA(50) ratios. We propose a counting frame that allows the comparison of the dose responses of the brain and cells to exogenous DHA.
Multifrequency bioelectrical impedance analysis in women with a normal and hypertensive pregnancy.

BACKGROUND An increase in total body water is common in normal pregnancy. It is thought to be an important mechanism of maternal adaptation to pregnancy. OBJECTIVE The aim of the present study was to assess longitudinal changes in body water compartments in pregnant women and to correlate these measurements with the course of pregnancy. DESIGN One hundred seventy-three pregnant women with apparently normal, single pregnancies participated in this longitudinal study. Anthropometric measurements and multifrequency bioelectrical impedance were performed during the first, second, and third trimesters of pregnancy. RESULTS One hundred three of the women completed all of the measurements; 50 of the women had a normal pregnancy and 13 had gestational hypertension. Total body water, extracellular water, and intracellular water values in normal pregnancies showed a significant, progressive increase throughout pregnancy. In women with gestational hypertension, total body water, extracellular water, and intracellular water values showed an opposite trend, suggesting a lack of plasma volume expansion through fluid-retention mechanisms. CONCLUSIONS Our results show that multifrequency bioelectrical impedance analysis can be used to monitor variations in body water compartments in normal pregnancy and detect gestational hypertension.
Estimation of the effect of the acute phase response on indicators of micronutrient status in Indonesian infants.

Many indicators of micronutrient status change during infection because of the acute phase response. In this study, relationships between the acute phase response, assessed by measuring concentrations of C-reactive protein (CRP), alpha(1)-antichymotrypsin (ACT) and alpha(1)-acid glycoprotein (AGP), and indicators of micronutrient status were analyzed in 418 infants who completed a 6-mo randomized, double-blind, placebo-controlled, supplementation trial with iron, zinc and/or beta-carotene. The acute phase response, defined by raised CRP (plasma concentration >10 mg/L), raised AGP (>1.2 g/L), or both raised CRP and AGP, significantly affected indicators of iron, vitamin A and zinc status, independently of the effects of supplementation. Plasma ferritin concentrations were higher by 15.7 (raised AGP) to 21.2 (raised CRP and AGP) micro g/L in infants with elevated acute phase proteins compared with infants without acute phase response (P < 0.001). In contrast, plasma concentrations of retinol were lower by 0.07 (P < 0.05, raised AGP) to 0.12 (P < 0.01, raised CRP) micro mol/L, and of zinc lower by 1.49 (P < 0.01, raised AGP) to 1.89 (P < 0.05, raised CRP and AGP) micro mol/L. Hemoglobin concentrations and the modified relative dose response were not affected. Consequently, the prevalence of iron deficiency anemia was underestimated in infants with raised acute phase proteins by >15%, whereas the prevalence of vitamin A deficiency was overestimated by >16% compared with infants without acute phase response. Hence, using indicators of micronutrient status without considering the effects of the acute phase response results in a distorted estimate of micronutrient deficiencies, whose extent depends on the prevalence of infection in the population.
Folate intake of the Dutch population according to newly established liquid chromatography data for foods.

BACKGROUND Determining folate intake is difficult because existing folate data in food-composition tables are scarce and unreliable. OBJECTIVE The purposes of this study were first to analyze 125 of the most important foods that contribute to folate intake in the Netherlands and second to estimate the folate intake of a representative sample of the population. DESIGN We analyzed the folate content of foods by using a newly developed HPLC trienzyme method combined with an affinity chromatography cleanup step. These results were then used to estimate the folate intake of persons aged 1-92 y who participated in the second Dutch National Food Consumption Survey (DNFCS) in 1992 (n = 6218). RESULTS For 35 important folate-containing foods, the mean relative folate contents measured by HPLC were 66%, 80%, and 77% of values for comparable foods included in the British food-composition table; the Ministry of Agriculture, Fisheries and Food table; and the US Department of Agriculture database, respectively. P values for comparison of relative values with 100% were 0.001, 0.171, and 0.144, respectively. The mean dietary folate intake of the DNFCS participants was 182 +/- 119 microg/d. Intake of supplement users (n = 86) was 344 microg/d, with 147 microg/d from supplements. On the basis of these findings, 42% of men and 54% of women do not meet current Dutch recommendations of 60 microg/d for children and 200 microg/d for adults. CONCLUSIONS Total folate quantities in foods, analyzed by HPLC, are approximately 25% lower than amounts listed in recent food-composition tables estimated by use of the microbiological method. On the basis of these new data, approximately 50% of a representative Dutch population sample does not meet the current recommendations for folate intake.
Decaying Indicators of Compromise

The steady increase in the volume of indicators of compromise (IoC) as well as their volatile nature makes their processing challenging. Once compromised infrastructures are cleaned up, threat actors are moving to on to other target infrastructures or simply changing attack strategies. To ease the evaluation of IoCs as well as to harness the combined analysis capabilities, threat intelligence sharing platforms were introduced in order to foster collaboration on a community level. In this paper, the open-source threat intelligence platform MISP is used to implement and showcase a generic scoring model for decaying IoCs shared within MISP communities matching their heterogeneous objectives. The model takes into account existing meta-information shared along with indicators of compromise,facilitating the decision making process for machines in regards to the validity of the shared indicator of compromise. The model is applied on common use-cases that are normally encountered during incident response.
MUC5B is the prominent mucin in human gallbladder and is also expressed in a subset of colonic goblet cells.

To elucidate the roles of human gallbladder mucin (HGBM), such as in gallstone formation and cytoprotection, it is essential to identify HGBM and study its expression. This was performed by metabolic labeling, Western blotting, immunohistochemistry, and RT-PCR. In a large number of individuals, antibodies against purified HGBM and against MUC5B detected a mucin precursor (∼470 kDa) in the gallbladder and colon, but not in the small intestine. In the gallbladder, Western blotting using specific anti-MUC5B antibodies showed that this mucin precursor represented an identical mucin, MUC5B. RT-PCR experiments demonstrated a similar tissue distribution pattern of MUC5BmRNA. Immunohistochemistry with anti-HGBM and anti-MUC5B showed staining in gallbladder epithelial cells and colonic goblet cells in the crypt base, but not in the small intestine; double labeling showed that HGBM was located in small granules within goblet cells, colocalizing to MUC2-containing goblet cells. Metabolic labeling demonstrated the secretion of mature MUC5B in the colon. Conclusively, MUC5B is identified as the prominent HGBM and is also expressed and secreted in the colon.
Hormonal regulation of ENaCs: insulin and aldosterone.

Although a variety of hormones and other agents modulate renal Na+ transport acting by way of the epithelial Na+ channel (ENaC), the mode(s), pathways, and their interrelationships in regulation of the channel remain largely unknown. It is likely that several hormones may be present concurrently in vivo, and it is, therefore, important to understand potential interactions among the various regulatory factors as they interact with the Na+transport pathway to effect modulation of Na+ reabsorption in distal tubules and other native tissues. This study represents specifically a determination of the interaction between two hormones, namely, aldosterone and insulin, which stimulate Na+ transport by entirely different mechanisms. We have used a noninvasive pulse protocol of blocker-induced noise analysis to determine changes in single-channel current ( i Na), channel open probability ( P o), and functional channel density ( N T) of amiloride-sensitive ENaCs at various time points following treatment with insulin for 3 h of unstimulated control and aldosterone-pretreated A6 epithelia. Independent of threefold differences of baseline values of transport caused by aldosterone, 20 nM insulin increased by threefold and within 10-30 min the density of the pool of apical membrane ENaCs ( N T) involved in transport. The very early (10 min) increases of channel density were accompanied by relatively small decreases of i Na(10-20%) and decreases of P o (28%) in the aldosterone-pretreated tissues but not the control unstimulated tissues. The early changes of i Na, P o, and N T were transient, returning very slowly over 3 h toward their respective control values at the time of addition of insulin. We conclude that aldosterone and insulin act independently to stimulate apical Na+ entry into the cells of A6 epithelia by increase of channel density.
World Health Organization equations have shortcomings for predicting resting energy expenditure in persons from a modern, affluent population: generation of a new reference standard from a retrospective analysis of a German database of resting energy expenditure.

BACKGROUND Reference standards for resting energy expenditure (REE) are widely used. Current standards are based on measurements made in the first part of the past century in various races and locations. OBJECTIVE The aim of the present study was to investigate the application of the World Health Organization (WHO) equations from 1985 in healthy subjects living in a modern, affluent society in Germany and to generate a new formula for predicting REE. DESIGN The study was a cross-sectional and retrospective analysis of data on REE and body composition obtained from 2528 subjects aged 5-91 y in 7 different centers between 1985 and 2002. RESULTS Mean REE varied between 5.63 and 8.07 MJ/d in males and between 5.35 and 6.46 MJ/d in females. WHO prediction equations systematically overestimated REE at low REE values but underestimated REE at high REE values. There were significant and independent effects of sex, age, body mass or fat-free mass, and fat mass on REE. Multivariate regression analysis explained up to 75% of the variance in REE. Two prediction formulas including weight, sex, and age or fat-free mass, fat mass, sex, and age, respectively, were generated in a subpopulation and cross-validated in another subpopulation. Significant deviations were still observed for underweight and normal-weight subjects. REE prediction formulas for specific body mass index groups reduced the deviations. The normative data for REE from the Institute of Medicine underestimated our data by 0.3 MJ/d. CONCLUSIONS REE prediction by WHO formulas systematically over- and underestimates REE. REE prediction from a weight group-specific formula is recommended in underweight subjects.