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In nature, liquids often circulate in channels textured with leaflets, cilia, or porous walls that deform with the flow. These soft structures are optimized to passively control flows and have inspired the design of novel microfluidic and soft-robotic devices. Yet, the relationship between the geometry of the soft structures and the flow properties remains so far poorly understood. Here, taking inspiration from the lymphatic system, we devise millifluidic valves, dressed with asymmetric soft leaflets that feature on-demand asymmetric flow properties, which we harness to induce flow rectification and pumping. We demonstrate that the functional mechanism at play involves an interplay between geometry, asymmetry, and fluid-structure interaction-induced nonlinearity. Our results open the way to a better characterization of biological leaflet malformations and to more accurate control of flows for microfluidics and soft-robotic systems.

Advancing our understanding of software vulnerabilities, automating their identification, the analysis of their impact, and ultimately their mitigation is necessary to enable the development of software that is more secure. While operating a vulnerability assessment tool that we developed and that is currently used by hundreds of development units at SAP, we manually collected and curated a dataset of vulnerabilities of open-source software and the commits fixing them. The data was obtained both from the National Vulnerability Database (NVD) and from project-specific Web resources that we monitor on a continuous basis. From that data, we extracted a dataset that maps 624 publicly disclosed vulnerabilities affecting 205 distinct open-source Java projects, used in SAP products or internal tools, onto the 1282 commits that fix them. Out of 624 vulnerabilities, 29 do not have a CVE identifier at all and 46, which do have a CVE identifier assigned by a numbering authority, are not available in the NVD yet. The dataset is released under an open-source license, together with supporting scripts that allow researchers to automatically retrieve the actual content of the commits from the corresponding repositories and to augment the attributes available for each instance. Also, these scripts allow to complement the dataset with additional instances that are not security fixes (which is useful, for example, in machine learning applications). Our dataset has been successfully used to train classifiers that could automatically identify security-relevant commits in code repositories. The release of this dataset and the supporting code as open-source will allow future research to be based on data of industrial relevance; also, it represents a concrete step towards making the maintenance of this dataset a shared effort involving open-source communities, academia, and the industry., Comment: This is a pre-print version of the paper that appears in the proceedings of The 16th International Conference on Mining Software Repositories (MSR), Data Showcase track

Cholesteryl ester transfer protein (CETP) plays an important role in plasma lipoprotein metabolism through its ability to transfer cholesteryl ester, triglyceride, and phospholipid between lipoproteins. CETP is a member of a gene family that also includes bactericidal/permeability-increasing protein (BPI). The crystal structure of BPI shows it to be composed of two domains that share a similar structural fold that includes an apolar ligand-binding pocket. As structurally important residues are conserved between BPI and CETP, it is thought that CETP and BPI may have a similar overall conformation. We have previously proposed a model of CETP structure based on the binding characteristics of anti-CETP monoclonal antibodies (mAbs). We now present a refined epitope map of CETP that has been adapted to a structural model of CETP that uses the atomic coordinates of BPI. Four epitopes composed of CETP residues 215-219, 219-223, 223-227, and 444-450, respectively, are predicted to be situated on the external surface of the central beta-sheet and a fifth epitope (residues 225-258) on an extended linker that connects the two domains of the molecule. Three other epitopes, residues 317-331, 360-366, and 393-410, would form part of the putative carboxy-terminal beta-barrel. The ability of the corresponding mAbs to compete for binding to CETP is consistent with the proximity of the respective epitopes in the model. These results thus provide experimental evidence that is consistent with CETP and BPI having similar surface topologies.

The aim of the present study was to investigate the role of the cholesteryl ester transfer protein (CETP) and the phospholipid transfer protein (PLTP) in determining the size distribution of high density lipoproteins (HDL) in human plasma. Whereas both purified CETP and PLTP preparations were able to promote the size redistribution of isolated HDL3, CETP favored the emergence of small HDL, while PLTP induced the formation of both small and large conversion products. When the total plasma lipoprotein fractions isolated from nine distinct subjects were incubated for 24 h at 37°C with either purified PLTP or purified CETP, significant alterations in the relative proportions of the five distinct plasma HDL subpopulations, i.e., HDL2b (9.71-12.90 nm), HDL2a (8.77-9.71 nm), HDL3a (8.17-8.77 nm), HDL3b (7.76-8.17 nm), and HDL3c (7.21-7.76 nm) were also observed. PLTP induced a significant increase in the relative abundance of HDL2b (8.66 ± 2.34% versus 7.87 ± 1.83% in controls; p

Abstract The relations between the level of plasma nonesterified fatty acid (NEFA) and both the mass concentration and activity of the cholesteryl ester transfer protein (CETP) were studied in fasted normolipidemic subjects. Plasma NEFA correlated positively with both CETP mass concentration ( r =.50; P HDL→VLDL+LDL activity) ( r =.46; P LDL→HDL activity) ( r =−.05; NS). The high binding capacity of albumin for NEFA was used to investigate whether lipoprotein-bound NEFAs were implicated in the modulation of the cholesteryl ester transfer reaction. As compared with nonsupplemented controls, the addition of an excess of fatty acid–free albumin (8 g/L) to total normolipidemic plasmas reduced CET HDL→VLDL+LDL activity (18.3±5.5% versus 9.8±3.1%; P LDL→HDL activity (22.3±4.5% versus 23.3±5.1%; NS). Moreover, CET HDL→VLDL+LDL and CET LDL→HDL activities correlated negatively when measured in native plasma ( r =−.45; P r =.40; P

The relations of cholesteryl ester transfer protein (CETP) activity to the distribution of low density lipoproteins (LDLs) and high density lipoproteins (HDLs) were investigated in fasting plasma samples from 27 normolipidemic subjects. LDL and HDL subfractions were separated by electrophoresis on 20-160 g/L and 40-300 g/L polyacrylamide gradient gels, respectively. Subjects were subdivided into two groups according to their LDL pattern. Monodisperse patterns were characterized by the presence of a single LDL band, whereas polydisperse patterns were characterized by the presence of several LDL bands of different sizes. To investigate the influence of lipid transfers on LDL patterns, total plasma was incubated at 37 degrees C in the absence of lecithin:cholesterol acyltransferase (LCAT) activity. The incubation induced a progressive transformation of polydisperse patterns into monodisperse patterns. Under the same conditions, initially monodisperse patterns remained unchanged. Measurements of the rate of radiolabeled cholesteryl esters transferred from HDL3s to very low density lipoproteins (VLDLs) and LDLs revealed that subjects with a monodisperse LDL pattern presented a significantly higher plasma CETP activity than subjects with a polydisperse LDL pattern (301 +/- 85%/hr per milliliter versus 216 +/- 47%/hr per milliliter, respectively; p < 0.02). In addition, when total plasma was incubated for 24 hours at 37 degrees C in the absence of LCAT activity, the relative mass of cholesteryl esters transferred from HDLs to apolipoprotein B-containing lipoproteins was greater in plasma with monodisperse LDL than in plasma with polydisperse LDL (0.23 +/- 0.06 versus 0.17 +/- 0.06, respectively; p < 0.02). These results indicated that in normolipidemic plasma, CETP could play an important role in determining the size distribution of LDL particles. The analysis of lipoprotein cholesterol distribution in the two groups of subjects sustained this hypothesis. Indeed, HDL cholesterol levels, the HDL:VLDL+LDL cholesterol ratio, and the esterified cholesterol:triglyceride ratio in HDL were significantly lower in plasma with the monodisperse LDL pattern than in plasma with the polydisperse LDL pattern (p < 0.01, p < 0.01, and p < 0.02, respectively). Plasma LCAT activity did not differ in the two groups. Plasma CETP activity correlated positively with the level of HDL3b (r = 0.542, p < 0.01) in the entire study population. Whereas plasma LCAT activity correlated negatively with the level of HDL2b (r = -0.455, p < 0.05) and positively with the levels of HDL2a (r = 0.475, p < 0.05) and HDL3a (r = 0.485, p < 0.05), no significant relation was observed with the level of HDL3b.(ABSTRACT TRUNCATED AT 400 WORDS)

The implication of cholesteryl ester transfer protein (CETP) in the high density lipoprotein (HDL) conversion process was studied by incubating HDL3 with a purified CETP preparation for 24 h at 37 degrees C. At a physiological plasma level, CETP induced a decrease of the HDL3 fraction (8.6 nm diameter) and the appearance of two new distinct particle subpopulations with mean diameters of 9.5 and 7.8 nm. To determine whether the effects of the CETP preparation could be assigned to CETP itself, the incubations were conducted either in the absence or in the presence of specific anti-CETP monoclonal antibodies. The HDL3 conversion process induced by the CETP preparation was totally blocked by addition to the incubation mixture of TP1 anti-CETP monoclonal antibody, known to completely inhibit the cholesteryl ester transfer activity in vitro. Moreover, the HDL conversion activity was retained, together with the CETP activity, on an anti-CETP affinity column and was insensitive to the presence of a lecithin:cholesterol acyltransferase inhibitor. Compared with incubations with CETP, incubations with CETP and apoA-IV increased the size range redistribution of the HDL3 particles, particularly by promoting the formation of very small-sized lipoprotein particles. The results of the study demonstrate thhat CETP can mediate an HDL size conversion even in the absence of lipid transfers between HDL and other lipoprotein fractions. They constitute a supplementary argument for a multipotential role of CETP in lipid transport.

Laboratoire de Biochimie des Lipoproteines, INSERM U498, Faculte de Medecine, Hopital du Bocage, Dijon, France.Cholesteryl ester transfer protein (CETP) and phospholipid transfer protein (PLTP) activities were measured in sera from 32 normolipidemic women and men consuming diets enriched in lauric, palmitic, or oleic acids. Serum CETP activity, measured as the rate of radiolabeled cholesteryl esters transferred from HDL toward serum apo B-containing lipoproteins, was higher with the palmitic acid diet (25.1+/-2.5%) than with the lauric acid (23.7+/-2.4%) and the oleic acid (24.0+/-2.7%) diets (P = 0.0028 and 0.0283, respectively). CETP mass concentrations, as measured with an enzyme-linked immunosorbent assay were increased after the lauric acid diet (2.57+/-0.63 mg/l) and the palmitic acid diet (2.49+/-0.64 mg/l) as compared with the oleic acid diet (2.34+/-0.45 mg/l) (P = 0.0035 and 0.0249, respectively). In contrast with CETP, serum PLTP activity, as measured as the rate of radiolabeled phosphatidylcholine transferred from liposomes toward serum HDL, was significantly higher with the lauric acid diet (23.5+/2.6%) than with the palmitic acid diet (22.5+/-2.5%) (P = 0.0013), while no significant differences were noted when comparing the saturated diets versus the oleic acid diet (23.0+/-2.3%). No significant alterations in the mean apparent diameter of LDL, and in the relative proportions of individual HDL subpopulations were observed from one dietary period to another. Nevertheless, lipid transfer activities correlated significantly with the relative abundance of HDL2b, HDL2a, HDL3b, and HDL3c, with opposite tendencies being observed for cholesteryl ester transfer and phospholipid transfer activities. In general, serum CETP activity correlated negatively with HDL cholesterol, but positively with triglyceride concentrations after the dietary interventions, and the relations with serum lipids were just the opposite for PLTP activity. In addition, CETP and PLTP activities correlated negatively when subjects consumed the standardized diets (P < 0.05 in all cases), but not when subjects consumed their habitual diet. It is concluded that serum lipid transfer activities in normolipidemic subjects can be significantly affected by the fatty acid content of the diet, with differential effects on CETP and PLTP activities.Publication Types: Clinical Trial

Cholesteryl ester and phospholipid transfer activities were determined in plasmas from 14 vertebrates, and lipid transfer values were analyzed in the light of the known atherogenesis susceptibility of studied species. Whereas cholesteryl ester transfer protein (CETP) and phospholipid transfer protein (PLTP) activities among vertebrate species were only measured in lipoprotein-deficient fractions in previous studies, both endogenous lipoprotein-dependent and endogenous lipoprotein-independent assays were used in the present work. In agreement with previous studies, a few species (chicken, man, rabbit and trout) displayed substantial CETP activity, whereas CETP activity was not detectable in other species (cow, dog, horse, mouse, pig, and rat). Additional species that were not studied before, i.e. cat, goat, and sheep, were shown to be deficient in plasma cholesteryl ester transfer activity, while duck was shown to constitute a new member of the high activity group. Unlike CETP activity, PLTP activity was detected in plasmas from all studied species, most of them being assayed here for the first time (cat, chicken, cow, duck, goat, horse, sheep, and trout). While dog, trout, mouse, and pig displayed the highest phospholipid transfer activity levels, the remarkable preservation of facilitated phospholipid transfers in plasma from all vertebrates might indicate an essential role of PLTP in vivo. Interestingly, animals with well-documented atherogenesis susceptibility (chicken, pig, rabbit, and man) displayed significantly higher mean CETP activity, but lower mean PLTP activity than known 'resistant' animals (cat, dog, mouse, and rat). In conclusion, the present study revealed marked differences in plasma lipid transfer activities between vertebrate species, and interspecies comparisons indicated that both CETP and PLTP may constitute two determinants of the atherogenicity of the plasma lipoprotein profile.

The aim of the present study was to investigate the role of the cholesteryl ester transfer protein (CETP) and the phospholipid transfer protein (PLTP) in determining the size distribution of high density lipoproteins (HDL) in human plasma. Whereas both purified CETP and PLTP preparations were able to promote the size redistribution of isolated HDL3, CETP favored the emergence of small HDL, while PLTP induced the formation of both small and large conversion products. When the total plasma lipoprotein fractions isolated from nine distinct subjects were incubated for 24 h at 37 degrees C with either purified PLTP or purified CETP, significant alterations in the relative proportions of the five distinct plasma HDL subpopulations, i.e., HDL2b (9.71-12.90 nm), HDL2a (8.77-9.71 nm), HDL3a (8.17-8.77 nm), HDL3b (7.76-8.17 nm), and HDL3c (7.21-7. 76 nm) were also observed. PLTP induced a significant increase in the relative abundance of HDL2b (8.66 +/- 2.34% versus 7.87 +/- 1. 83% in controls; p0.01) and a significant decrease in the relative abundance of HDL3a (32.76 +/- 3.42% versus 37.87 +/- 2.62% in controls; p0.05). In contrast, CETP significantly reduced the relative proportion of HDL2a (33.03 +/- 2.53% versus 37.56 +/- 6.43% in controls; p0.01) but significantly increased the relative proportion of both HDL3b (21.36 +/- 6.97% versus 15.58 +/- 7.75% in controls; p0.01) and HDL3c (3.21 +/- 4.84% versus 1.13 +/- 0.56% in controls; p0.05). Finally, in order to assess further the physiological relevance of in vitro observations, CETP activity, PLTP activity, and HDL size distribution were determined in plasmas from 33 alcoholic patients entering a cessation program. Alcohol withdrawal was associated with (i) a significant increase in plasma CETP activity (173.5 +/- 70.5%/h/ml before versus 223.2 +/- 69. 3%/h/ml after alcohol withdrawal, p = 0.0007), (ii) a significant reduction in plasma PLTP activity (473.9 +/- 203.7%/h/ml before versus 312.7 +/- 148.4%/h/ml after alcohol withdrawal, p = 0.0001), and (iii) a significant shift of large HDL2b and HDL2a toward small HDL3b and HDL3c. On the one hand, changes in plasma CETP activity correlated negatively with changes in the proportion of HDL2a (r = -0.597, p = 0.0002) and positively with changes in the proportion of HDL3b (r = 0.457, p = 0.0075). On the other hand, changes in plasma PLTP activity correlated positively with changes in the proportion of HDL2b (r = 0.482, p = 0.0045) and negatively with changes in the proportion of HDL3a (r = -0.418, p = 0.0154). Taken together, data of the present study revealed that plasma PLTP and CETP can exert opposite effects on the size distribution of plasma HDL. PLTP can promote the formation of HDL2b particles at the expense of HDL3a, while CETP can promote the formation of HDL3b particles at the expense of HDL2a.

The present report describes the first competitive enzyme-linked immunosorbent assay (ELISA) for the cholesteryl ester transfer protein (CETP), an enzyme playing an important role in lipoprotein metabolism. This assay was developed with well-characterized TP1 anti-CETP monoclonal antibodies. The sensitivity of the ELISA assay was comparable with the sensitivity of the previously described radioimmunoassays since 1 ng of CETP per microwell of the immunoplate could be detected. Intra- and inter-assay coefficients of variation were 4% and 6%, respectively. This enzyme immunoassay provides a specific, sensitive and reproducible method for measuring CETP concentrations in various biological samples. Within normolipidemic subjects, the mean (+/- S.D.) of the plasma CETP concentration was 2.77 (+/- 0.59) micrograms/ml with a range of 1.87 to 4.23 micrograms/ml. When plasmas were supplemented with fatty acid-free albumin, the positive correlation observed between plasma CETP mass and CETP activity was improved, suggesting that plasma non-esterified fatty acids could play a role in modulating the activity of the cholesteryl ester transfer protein. When applied to the study of the binding of CETP to lipoprotein substrates, the enzyme immunoassay revealed that the experimental protocol used to separate lipoprotein fractions can have a great influence on the plasma distribution of CETP.

The aim of the present study was to determine in vitro the effects of various purified apolipoproteins (apo) on the activity of the cholesteryl ester transfer protein (CETP). It appeared that the ability of apoA-I, A-II, and A-IV to modulate the CETP-mediated transfer of radiolabeled cholesteryl esters between low density lipoproteins (LDL) and high density lipoproteins (HDL) was markedly influenced by the final apolipoprotein:lipoprotein ratio in incubation mixtures. At low apolipoprotein:lipoprotein ratio, the rate of radiolabeled cholesteryl esters transferred from HDL3 to LDL was significantly increased in the presence of apoA-I and apoA-IV. Under similar conditions, the rate of radiolabeled cholesteryl esters transferred from LDL to HDL3 was increased in the presence of apoA-I while apoA-IV had no significant effects. At high apolipoprotein:lipoprotein ratio, the ability of apoA-I and apoA-IV to enhance the rate of radiolabeled cholesteryl esters transferred either from HDL3 to LDL or from LDL to HDL3 was considerably reduced. At the highest apolipoprotein:lipoprotein ratio studied, apoA-I and A-IV became inhibitors of the CETP-mediated transfer reaction. Interestingly, apoA-II differed markedly from other apolipoproteins as, even at a low apolipoprotein:lipoprotein ratio, it significantly inhibited CETP activity as measured either from HDL3 to LDL or from LDL to HDL3. The inhibition by apoA-II was concentration-dependent and, at the highest apolipoprotein:lipoprotein ratio studied, cholesteryl ester transfer activity was totally suppressed. The possibility of a direct interaction between CETP and the two major HDL apolipoproteins, apoA-I and apoA-II, was further investigated by combining crosslinking and immunoblotting techniques. Whereas CETP alone had an apparent molecular mass of 76,000 +/- 3,100 Da, crosslinking reactions in incubation mixtures containing CETP and either apoA-I or apoA-II revealed the appearance of additional protein bands with apparent molecular masses of 99,600 +/- 6,100 and 86,900 +/- 4,500 Da, respectively. These complexes corresponded to the association of one molecule of CETP with one molecule of apoA-I or apoA-II. Interestingly, the mass concentrations of apoA-II needed to produce visible CETP-apolipoprotein complexes appeared to be about ten times higher as compared with apoA-I, suggesting that CETP may have a lower affinity for apoA-II than for apoA-I. In conclusion, data from the present study indicate that apolipoproteins A-I, A-II, and A-IV could be potent modulators of the CETP-mediated transfer of cholesteryl esters between HDL and LDL fractions.(ABSTRACT TRUNCATED AT 400 WORDS)