Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) ...characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.
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G-Free Onarlioglu, Kaan; Bilge, Leyla; Lanzi, Andrea ...
Proceedings of the 26th Annual Computer Security Applications Conference,
12/2010
Conference Proceeding
Despite the numerous prevention and protection mechanisms that have been introduced into modern operating systems, the exploitation of memory corruption vulnerabilities still represents a serious ...threat to the security of software systems and networks. A recent exploitation technique, called Return-Oriented Programming (ROP), has lately attracted a considerable attention from academia. Past research on the topic has mostly focused on refining the original attack technique, or on proposing partial solutions that target only particular variants of the attack.
In this paper, we present G-Free, a compiler-based approach that represents the first practical solution against any possible form of ROP. Our solution is able to eliminate all unaligned free-branch instructions inside a binary executable, and to protect the aligned free-branch instructions to prevent them from being misused by an attacker. We developed a prototype based on our approach, and evaluated it by compiling GNU libc and a number of real-world applications. The results of the experiments show that our solution is able to prevent any form of return-oriented programming.
Currently used screening criteria for retinopathy of prematurity (ROP) show high sensitivity for predicting treatment-requiring ROP but low specificity; over 90% of examined infants do not develop ...ROP that requires treatment (type 1 ROP). A novel weight gain-based prediction model was developed by the G-ROP study group to increase the specificity of the screening criteria and keep the number of ophthalmic examinations as low as possible. This retrospective cohort study aimed to externally validate the G-ROP screening criteria in a Swiss cohort.
Data from 645 preterm infants in ROP screening at Inselspital Bern between January 2015 and December 2019 were retrospectively retrieved from the screening log and analysed. The G-ROP screening criteria, consisting of 6 trigger parameters, were applied in infants with complete data. To determine the performance of the G-ROP prediction model for treatment-requiring ROP, sensitivity and specificity were calculated.
Complete data were available for 322 infants who were included in the analysis. None of the excluded infants had developed type 1 ROP. By applying the 6 criteria in the G-ROP model, 214 infants were flagged to undergo screening: among these, 14 developed type 1 ROP, 9 developed type 2 ROP, and 43 developed milder stages of ROP. The sensitivity for predicting treatment-requiring ROP was 100% (CI, 0.79-1.00), and the specificity was 41% (CI, 0.35 -0.47). Implementing the novel G-ROP screening criteria would reduce the number of infants entering ROP screening by approximately one third.
The overall prevalence of treatment-requiring ROP was low (2.15%). Previously published performance parameters for the G-ROP algorithm were reproducible in this Swiss cohort. Importantly, all treatment-requiring infants were correctly identified. By using these novel criteria, the burden of screening examinations could be significantly reduced.
Background: Small monomeric GTPases act as molecular switches in several processes that involve polar cell growth, participating mainly in vesicle trafficking and cytoskeleton rearrangements. This ...gene superfamily has largely expanded in plants through evolution as compared with other Kingdoms, leading to the suggestion that members of each subfamily might have acquired new functions associated to plant-specific processes. Legume plants engage in a nitrogen-fixing symbiotic interaction with rhizobia in a process that involves polar growth processes associated with the infection throughout the root hair. To get insight into the evolution of small GTPases associated with this process, we use a comparative genomic approach to establish differences in the Ras GTPase superfamily between legume and non-legume plants.
Results: Phylogenetic analyses did not show clear differences in the organization of the different subfamilies of small GTPases between plants that engage or not in nodule symbiosis. Protein alignments revealed a strong conservation at the sequence level of small GTPases previously linked to nodulation by functional genetics. Interestingly, one Rab and three Rop proteins showed conserved amino acid substitutions in legumes, but these changes do not alter the predicted conformational structure of these proteins. Although the steady-state levels of most small GTPases do not change in response to rhizobia, we identified a subset of Rab, Rop and Arf genes whose transcript levels are modulated during the symbiotic interaction, including their spatial distribution along the indeterminate nodule.
Conclusions: This study provides a comprehensive study of the small GTPase superfamily in several plant species. The genetic program associated to root nodule symbiosis includes small GTPases to fulfill specific functions during infection and formation of the symbiosomes. These GTPases seems to have been recruited from members that were already present in common ancestors with plants as distant as monocots since we failed to detect asymmetric evolution in any of the subfamily trees. Expression analyses identified a number of legume members that can have undergone neo- or sub-functionalization associated to the spatio-temporal transcriptional control during the onset of the symbiotic interaction.
Regulation of plant cell wall deposition and patterning is essential for the normal growth and development of plants. Small GTPases play pivotal roles in the modulation of primary cell wall formation ...by controlling cytoskeletal organization and membrane trafficking. However, the functions of small GTPases in secondary cell wall development are poorly understood. Recent studies on xylem cells revealed that the Rho of plants (ROP) group of small GTPases critically participates in the spatial patterning of secondary cell walls. In differentiating xylem cells, a specific GTPase-activating protein (GAP)/guanine nucleotide exchange factor (GEF) pair facilitates local activation of ROP11 to establish de novo plasma membrane domains. The activated ROP11 then recruits a microtubule-associated protein, MIDD1, to mediate the mutual inhibition between cortical microtubules and active ROP. Furthermore, recent works suggest that certain small GTPases, including ROP and Rab GTPases, regulate membrane trafficking to establish secondary cell wall deposition and patterning. Accordingly, this mini-review assesses and summarizes the current literature regarding the emerging functions of small GTPases in the development of secondary cell walls.
Single‐step process for production of porous scaffold based on poly(pentadecanolide) (PPDL) is reported. The scaffold is produced via in situ porosity generation during ring‐opening polymerization ...(ROP) of the lactone pentadecanolide (PDL) in high internal phase emulsion (HIPE) using a water soluble enzyme (Lipase TL) as catalyst. The enzyme present in dispersed aqueous phase of HIPE effectively carries out ROP of monomer present in continuous oil phase. The polymerization occurs at the interface of oil and water in HIPE and complete monomer conversion is achieved in 96 h at 40 °C. Porous scaffold having interconnected pores is obtained as the final product and formation of PPDL is confirmed by spectroscopic and thermal analysis. The process thus developed is a single‐step process to produce porous scaffolds via ROP of a lactone that can be extended to see its efficacy using monomer‐soluble organometallic catalysts and monomers other than PDL including lactones, lactides, and cyclic carbonates.
A single step solvent free process to create porous scaffold of an aliphatic polyester, poly(pentadecanolide) is devised. Scaffold is developed via in situ pore formation during ring‐opening polymerization (ROP) of high internal phase emulsion (HIPE) of pentadecanolide comprising continuous phase and catalyst, Lipase TL, present in dispersed aqueous phase. HIPE‐ROP may further be extended for fabrication of scaffolds based on other lactones and lactides.
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Modern polymeric material design often involves precise tailoring of molecular/supramolecular structures which is also called macromolecular engineering. The available tools for molecular structure ...tailoring are controlled/living polymerization methods, click chemistry, supramolecular polymerization, self-assembly, among others. When polymeric materials with complex molecular architectures are targeted, it usually takes several steps of reactions to obtain the aimed product. Concurrent polymerization methods, i.e., two or more reaction mechanisms, steps, or procedures take place simultaneously instead of sequentially, can significantly reduce the complexity of the reaction procedure or provide special molecular architectures that would be otherwise very difficult to synthesize. Atom transfer radical polymerization, ATRP, has been widely applied in concurrent polymerization reactions and resulted in improved efficiency in macromolecular engineering. This perspective summarizes reported studies employing concurrent polymerization methods with ATRP as one of the reaction components and highlights future research directions in this area.
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The current study investigates the wear life of button bits and rate of penetration (ROP) of rotary-percussive drilling machines by employing geotechnical rock properties. According to the research ...plan, three hydropower projects and six active mining quarries in Pakistan were included. The field work included recording of drill bit consumption (m/bit) and measurement of penetration rate (m/min) from the 11 selected rock units. A comprehensive laboratory testing plan on the collected rock units was carried out to include rock abrasivity assessment CERCHAR (CAI), LCPC (ABR) and abrasion value steel (AVS) tests, NTNU/SINTEF drillability parameters Sievers’ J-value (SJ), brittleness value (S
20
), Cutter Life Index™ (CLI) and Drilling Rate Index™ (DRI) and physico-mechanical properties uniaxial compressive strength (UCS), Brazilian tensile strength (BTS), porosity (n), density (ρ), p wave velocity (Vp), Schmidt rebound hardness (SRH) and brittleness index (B
3
). Moreover, XRD analyses were performed to compute equivalent quartz content (EQC %), rock abrasivity index (RAI) and Vickers hardness number of rock (VHNR). The least square regression technique was employed to predict bit life from geotechnical rock properties. Dependence of ROP on geotechnical rock parameters was also discussed. Finally, two multiple linear regression models were also proposed for the estimation of bit life based on the included geotechnical rock properties. The developed multi-variable models were validated using the F-test statistical method. The correlations so developed are particularly proposed for rock engineers involved in rock drilling projects.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Three series of polyesters based on monomer combinations of ε-caprolactone (ε-CL), ethylene brassylate (EB), and l-Lactide (LLA) with the alkyl substituted lactone ε-decalactone (ε-DL) were ...synthesized at different molar ratios. Copolymers were obtained via ring opening polymerization (ROP) employing TBD (1,5,7-triazabicyclo-4.4.0-dec-5-ene), an organic catalyst which can be handled under normal conditions, avoiding the use of glove box equipment. The molar monomer composition of resulting copolymers differed from theoretical values due to lower ε-DL reactivity; their Mn and Mw values were up to 14 kDa and 22.8 kDa, respectively, and distributions were (Ɖ) ≤ 2.57. The thermal stability of these materials suffered due to variations in their ε-DL molar content. Thermal transitions such as melting (Tm) and crystallization (Tc) showed a decreasing tendency as ε-DL molar content increased, while glass transition (Tg) exhibited minor changes. It is worth mentioning that changes in monomer composition in these polyesters have a strong impact on their thermal performance, as well as in their crystallization degree. Consequently, variations in their chemical structure may have an effect on hydrolyic degradation rates. It should be noted that, in future research, some of these copolymers will be exposed to hydrolytic degradation experiments, including characterizations of their mechanical properties, to determine their adequacy in potential use in the development of soft medical devices.
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Five novel air- and moisture-stable polymetallic Ti and Zr amino acid-derived amine bis(phenolate) (ABP) complexes were synthesised and fully characterised, including X-ray crystallographic studies. ...The reaction of the ABP proligands with Ti or Zr alkoxides has resulted in the formation of polymetallic aggregates of different nuclearity. The steric bulk on the pendant arm of the ligand was found to play a critical role in establishing the nuclearity of the aggregated complex. Sterically, less-demanding groups, such as H or Me, facilitated the formation of tetrametallic Ti clusters, bridged by carboxylate groups, while increased steric bulk (tBu) led to the formation of binuclear μ-oxo-bridged species. The isolated complexes were employed as catalysts for the ring opening polymerisation (ROP) of rac-lactide. Overall, the Ti catalysts were all active with the smaller, bimetallic Ti aggregates exhibiting relatively faster rates. A monometallic, bis(ABP) Zr complex was found to exert remarkable ROP activity, albeit with limited control over the tacticity and molecular weight distribution of the polymer. A further oxo-bridged Zr cluster was shown to display a previously unprecedented trimetallic structure and achieved a moderate rate in the ROP of rac-lactide.
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