Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Drosophila Rab5 during endosomal trafficking at the synapse and evoked neurotransmitter release

During constitutive endocytosis, internalized membrane traffics through endosomal compartments. At synapses, endocytosis of vesicular membrane is temporally coupled to action potential–induced exocytosis of synaptic vesicles. Endocytosed membrane may immediately be reused for a new round of neurotransmitter release without trafficking through an endosomal compartment. Using GFP-tagged endosomal markers, we monitored an endosomal compartment in Drosophila neuromuscular synapses. We showed that in conditions in which the synaptic vesicles pool is depleted, the endosome is also drastically reduced and only recovers from membrane derived by dynamin-mediated endocytosis. This suggests that membrane exchange takes place between the vesicle pool and the synaptic endosome. We demonstrate that the small GTPase Rab5 is required for endosome integrity in the presynaptic terminal. Impaired Rab5 function affects endo- and exocytosis rates and decreases the evoked neurotransmitter release probability. Conversely, Rab5 overexpression increases the release efficacy. Therefore, the Rab5-dependent trafficking pathway plays an important role for synaptic performance.
Genetic Analysis of Root and Shoot Traits in the ‘Essex’ By ‘Forrest’ Recombinant Inbred Line (RIL) Population of Soybean [Glycine max (L.) Merr.]

Crop productivity is severely reduced by water deficit and drought in many plant species including soybean. Improved root and shoot traits can contribute to drought tolerance ability of the plant. This research was conducted to identify QTL that underlie several root and shoot traits in the ‘Essex’ by ‘Forrest’ (ExF RILs, n=94) recombinant inbred line (RIL) soybean population. Field collected samples were used for gathering phenotypic data of basal root thickness (BRT), lateral root number (LRN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW), and calculating RFW/SFW, and RDW/SDW ratios. All traits and ratios were compared against DNA markers using the composite interval mapping (CIM). A total of 12 QTL: 3 for MRL, 1 QTL for LRN, 1 QTL for BRT, 2 QTL for RFW, 2 QTL for RDW, 4 QTL for SFW, 3 QTL for SDW, and 3 QTL for SFW/SDW were identified and mapped on different linkage groups (LGs) A2, B2, C2, D1a, F, G, and N. The LOD scores of these QTL ranged from 2.5 to 6.0. No QTL were associated with RFW/RDW. The root and shoot trait QTL of this study may benefit breeding programs for producing cultivars tolerant to water deficit and high yield. Preliminary analyses of genes the QTL regions using GO annotation gave insight into genes that may underlie some of these QTLs.
Catalytic strategy for carbon−carbon bond scission by the cytochrome P450 OleT

Significance The biocatalytic production of hydrocarbons from abundant natural resources provides a means to expand the current fuel inventory. The recently identified cytochrome P450, OleT, synthesizes 1-alkenes from fatty acids through a carbon−carbon scission reaction that is highly atypical for the enzyme superfamily. Rapid kinetics studies reveal two critical reaction cycle intermediates that define the catalytic strategy used by OleT and highlight the functional versatility of P450 enzymes. OleT is a cytochrome P450 that catalyzes the hydrogen peroxide-dependent metabolism of Cn chain-length fatty acids to synthesize Cn-1 1-alkenes. The decarboxylation reaction provides a route for the production of drop-in hydrocarbon fuels from a renewable and abundant natural resource. This transformation is highly unusual for a P450, which typically uses an Fe4+−oxo intermediate known as compound I for the insertion of oxygen into organic substrates. OleT, previously shown to form compound I, catalyzes a different reaction. A large substrate kinetic isotope effect (≥8) for OleT compound I decay confirms that, like monooxygenation, alkene formation is initiated by substrate C−H bond abstraction. Rather than finalizing the reaction through rapid oxygen rebound, alkene synthesis proceeds through the formation of a reaction cycle intermediate with kinetics, optical properties, and reactivity indicative of an Fe4+−OH species, compound II. The direct observation of this intermediate, normally fleeting in hydroxylases, provides a rationale for the carbon−carbon scission reaction catalyzed by OleT.
Investigation of a pulsed-plasma jet for shock / boundary layer control

Pulsed jets with peak exit velocities as high as 250 m/s are generated by rapidly heating the air inside a chamber with an electrical discharge. The heated pressurized gas issues from a small orifice to form the pulsed plasma jet or ‘spark jet’. Pulsing frequencies as high as 5 kHz are obtained. An array of these jets, in a pitched and skewed configuration, is used to force the unsteady motion of the interaction formed by a 24° compression ramp in a Mach 3 flow. The Reynolds number of the incoming boundary layer is Re=3300. The effect of the plasma jet array on the separation shock motion is studied by using 10 kHz Schlieren imaging and fast-response wall pressure measurements. Results show that when the pulsed jet array is placed upstream of the interaction, the jets cause the separation shock to move in a quasi-periodic manner, i.e., nearly in sync with the pulsing cycle. As the jet fluid convects across the separation shock, the shock responds by moving upstream, which is primarily due to the presence of hot gas and hence the lower effective Mach number of the incoming flow. Once the hot gases pass through the interaction, t he separation shock recovers by moving downstream, and this recovery velocity is approximately 1% to 3% of the free stream velocity. With forcing, the low-frequency energy content of the pressure fluctuations at a given location under the intermittent region decreases significantly. This is believed to be a result of an increase in the mean scale of the interaction under forced conditions. Pulsed-jet injection was also employed within the separation bubble, but negligible changes to the separation shock motion were observed . These results indicate that influencing the dynamics of this compression ramp interaction is much more effective by placing the actuator in the upstream boundary layer.
Polydopamine-Inspired Surface Modification of Polypropylene Hernia Mesh Devices via Cold Oxygen Plasma: Antibacterial and Drug Release Properties

Mesh infection is a major complication of hernia surgery after polypropylene (PP) mesh implantation. Modifying the PP mesh with antibacterial drugs is an effective way to reduce the chance of infection, but the hydrophobic characteristic of PP fibers has obstructed the drug adhesion. Therefore, to prepare antimicrobial PP mesh with a stable drug coating layer and to slow the drug release property during the hernia repair process has a great practical meaning. In this work, PP meshes were coated by bio-inspired polydopamine (PDA), which can load and release levofloxacin. PP meshes were activated with cold oxygen plasma and then plasma activated PP fibers were coated with PDA. The PDA coated meshes were further soaked in levofloxacin. The levofloxacin loaded PP meshes demonstrate excellent antimicrobial properties for 6 days and the drug release has lasted for at least 24 h. Moreover, a control PP mesh sample without plasma treatment was also prepared, after coating with PDA and loading levofloxacin. The antimicrobial property was sustained only for two days. The maximum inhibition zone of PDA coated meshes with and without plasma treatment was 12.5 and 9 mm, respectively. On all accounts, the modification strategy can facilely lead to long-term property of infection prevention.
Analysis of essential oil of eaglewood tree (Aquilaria agallocha Roxb.) by gas chromatography mass spectrometry

The study was carried out to find out the differences in composition of oils obtained from healthy, naturally infected and artificially screws wounds eaglewood ( Aquilaria agallocha Roxb.) using gas chromatography mass spectrometry (GC-MS) analysis. Natural healthy plants agar contained octacosane (19.83%), naphthalene, 1,2,3,5,6,7,8,8a-octahydro-1,8a-dimethyl-7-(1-methylethenyl)-, [1R-(1.alpha.,7.beta.,8a.alpha.)]- (12.67%), 5-isobutyramido-2-methyl pyrimidine (13.52%), caryophyllene oxide (11.25%) and (.+-.)-cadinene (5.46%). Natural infected plants agar (super agar) contained cycloheptane, 4-methylene-1-methyl-2-(2-methyl-1-propen-1-yl)-1-vinyl- (46.17%), caryophyllene oxide (33.00%) and 7-Isopropenyl-4a-methyl-1-methylenedecahydronaphthalene (20.83%). Artificially screw injected plants agar contained diisooctyl phthalate (71.97%), 1H-Cycloprop[e]azulen-4-ol, decahydro-1,1,4,7-tetramethyl-, [1ar-(1a.alpha.,4.beta.,4a.beta., 7.alpha., 7a.beta., 7b.alpha.)]- (9.16%), hexadecanoic acid (7.05%), naphthalene, 1,2,3,5,6,7,8,8a-octahydro-1,8a-dimethyl-7-(1-methylethenyl)-, [1R-(1.alpha.,7.beta.,8a.alpha.)]- (6.45%) and aristolene (5.36%). This study showed a marked difference in the oil compositions among the treatments with regards to their quality.
Risk of acute myocardial infarction, stroke, heart failure, and death in elderly Medicare patients treated with rosiglitazone or pioglitazone.

CONTEXT Studies have suggested that the use of rosiglitazone may be associated with an increased risk of serious cardiovascular events compared with other treatments for type 2 diabetes. OBJECTIVE To determine if the risk of serious cardiovascular harm is increased by rosiglitazone compared with pioglitazone, the other thiazolidinedione marketed in the United States. DESIGN, SETTING, AND PATIENTS Nationwide, observational, retrospective, inception cohort of 227,571 Medicare beneficiaries aged 65 years or older (mean age, 74.4 years) who initiated treatment with rosiglitazone or pioglitazone through a Medicare Part D prescription drug plan from July 2006-June 2009 and who underwent follow-up for up to 3 years after thiazolidinedione initiation. MAIN OUTCOME MEASURES Individual end points of acute myocardial infarction (AMI), stroke, heart failure, and all-cause mortality (death), and composite end point of AMI, stroke, heart failure, or death, assessed using incidence rates by thiazolidinedione, attributable risk, number needed to harm, Kaplan-Meier plots of time to event, and Cox proportional hazard ratios for time to event, adjusted for potential confounding factors, with pioglitazone as reference. RESULTS A total of 8667 end points were observed during the study period. The adjusted hazard ratio for rosiglitazone compared with pioglitazone was 1.06 (95% confidence interval [CI], 0.96-1.18) for AMI; 1.27 (95% CI, 1.12-1.45) for stroke; 1.25 (95% CI, 1.16-1.34) for heart failure; 1.14 (95% CI, 1.05-1.24) for death; and 1.18 (95% CI, 1.12-1.23) for the composite of AMI, stroke, heart failure, or death. The attributable risk for this composite end point was 1.68 (95% CI, 1.27-2.08) excess events per 100 person-years of treatment with rosiglitazone compared with pioglitazone. The corresponding number needed to harm was 60 (95% CI, 48-79) treated for 1 year. CONCLUSION Compared with prescription of pioglitazone, prescription of rosiglitazone was associated with an increased risk of stroke, heart failure, and all-cause mortality and an increased risk of the composite of AMI, stroke, heart failure, or all-cause mortality in patients 65 years or older.
The Cauchy problem for the Benjamin-Ono equation in $L^2$ revisited

In a recent work, Ionescu and Kenig proved that the Cauchy problem associatedto the Benjamin-Ono equation is well-posed in $L^2(\mathbb R)$. In this paper we give a simpler proof of Ionescu and Kenig's result, which moreover provides stronger uniqueness results. In particular, we prove unconditional well-posedness in $H^s(\mathbb R)$, for $s>1/4$.
Effects of Natural Bioactive Products on the Growth and Ginsenoside Contents of Panax ginseng Cultured in an Aeroponic System

This study was conducted to evaluate the effects of natural bioactive products such as Manda enzyme (T1), Yangmyeongwon (T2), effective microorganisms (T3), and Kelpak (T4) on the growth and ginsenoside contents of Panax ginseng cultured in an aeroponic system using a two-layer vertical type of nutrient bath under natural light conditions. The growth of ginseng plants showed specific characteristics according to the positions in which they were cultured due to the difference of light transmittance and temperature in the upper and lower layers during aeroponic culture in a two-layer vertical type of system. The growth of the aerial part of the leaves and stems of ginseng plants cultured in the lower layer (4,000 to 6,000 lx, 23℃ to 26℃) of the nutrient bath was observed to be superior to that of the ginseng plants cultured in the upper layer (12,000 to 15,000 lx, 25℃ to 28℃). The leaf area was significantly larger in the treatment of T2 and T4 (46.70 cm2) than with other treatments. Conversely, the values of the root weight and root diameter were higher in ginseng plants cultured in the upper layer of the nutrient bath. The root weight was significantly heavier in the treatment of T4 (6.46 g) and T3 (6.26 g) than with other treatments. The total ginsenoside content in the leaves and roots was highest in the ginseng plants cultured by the treatment of T1, at 16.20%, while the total ginsenoside content obtained by other treatments decreased in the order of T4, T5 (control), T2, and T3, at 13.21%, 12.30%, 14.84%, and 14.86%, respectively. The total ginsenoside content of the ginseng leaves was found to be significantly higher in the treatment of T1 in the lower layer of the nutrient bath, at 15.30%, while the content of the ginseng roots in the treatments of T3 and T4, at 1.27% and 1.23%, respectively, was significantly higher than in other treatments in the upper layer of the nutrient bath.
Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2‐3)Gal: a study by in silico mutations and molecular dynamics simulations

Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM‐PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics. Copyright © 2014 John Wiley & Sons, Ltd.
Optimal management of hypothyroidism, hypothyroxinaemia and euthyroid TPO antibody positivity preconception and in pregnancy

Normal physiological changes of pregnancy warrant the need to employ gestation specific reference ranges for the interpretation of thyroid function tests. Thyroid hormones play crucial roles in foetal growth and neurodevelopment which are dependent on adequate supply of maternal thyroid hormones from early gestation onwards. The prevention of significant adverse obstetric and neurodevelopmental outcomes from hypothyroidism requires a strategy of empirical levothyroxine dose increases and predictive dose adjustments in pregnancy combined with regular thyroid function testing, starting before pregnancy and until the postpartum period. Subclinical hypothyroidism has been associated with an increased risk of pregnancy loss and neurocognitive deficits in children, especially when diagnosed before or during early pregnancy. Whilst trials of levothyroxine replacement for mild hypothyroidism in pregnancy have not indicated definite evidence of improvements in these outcomes, professional guidelines recommend treatment, especially if evidence of underlying thyroid autoimmunity is present. Studies of isolated hypothyroxinaemia in pregnancy have shown conflicting evidence with regards to adverse obstetric and neurodevelopmental outcomes and no causative relationships have been determined. Treatment of this condition in pregnancy may be considered in those with underlying thyroid autoimmunity. Whilst the evidence for a link between the presence of anti‐TPO antibodies and increased risks of pregnancy loss and infertility is compelling, the results of ongoing randomized trials of levothyroxine in euthyroid women with underlying autoimmunity are currently awaited. Further studies to define the selection of women who require levothyroxine replacement and to determine the benefits of a predictive dose adjustment strategy are required.
In vitro determination of the antibiotic susceptibility of biofilm-forming Pseudomonas aeruginosa and Staphylococcus aureus: possible role of proteolytic activity and membrane lipopolysaccharide

We carried out a comprehensive overview of inhibitory effects of selected antibiotics on planktonic and biofilm cells of Staphylococcus aureus (ATCC 29213) and Pseudomonas aeruginosa (ATCC 27853) strains. The possible involvement of protease activity and the lipopolysaccharide (LPS) profile of P. aeruginosa were also analyzed. Biofilm cells of both strains were more resistant to antibiotics than their planktonic counterparts. Protease activity was increased in both strains in the biofilm forms. Challenge with sublethal doses of antibiotics also increased proteolytic activity of biofilm cells. Additionally, the LPS profile of P. aeruginosa showed pattern alterations of the biofilm that can contribute to biofilm resistance and survival. These observations provide evidence for the involvement of bacterial proteolytic activity and LPS profile in the resistance of biofilm bacteria to antibiotics compared to their planktonic counterparts.
Effect of Pattern Coating Thickness on Surface Roughness and Porosity of Nodular Cast Iron (FCD) 450 Using Lost Foam Casting Method

Lost foam casting is one of casting method that uses expanded polystyrene (EPS) foam as a mold pattern and embedded into silica sand. When the molten metal is poured into a mold, EPS will melt and evaporate, so the cavity is filled by the molten metal. The main objective of this research was to investigate the effect of pattern coating thickness on surface roughness and porosity of nodular cast iron FCD 450 by using the lost foam casting method. The mold pattern of EPS foam has 17 kg/m3 of density and 3-24 mm of section thickness. Coating material was used a refractory material of Zircon (ZrO2) and binder of Colloidal Silica (O2Si). In order to study effects of coating thickness, experiments were conducted with of 0-1300 μm. FCD 450 metal alloy was melted in a crucible furnace and the molten metal was poured into a mold at temperatures of 1350 °C-1450 °C. The experimental results showed the surface roughness decreases with increasing coating thickness of the EPS pattern. Uncoated of EPS pattern influenced the casting quality. The porosity increases with coating thickness of EPS pattern.
Converging on the optimal attainment of requirements

Planning for the optimal attainment of requirements is an important early lifecycle activity. However, such planning is difficult when dealing with competing requirements, limited resources, and the incompleteness of information available at requirements time. A novel approach to requirements optimization is described. A requirements interaction model is executed to randomly sample the space of options. This produces a large amount of data, which is then condensed by a summarization tool. The result is a small list of critical decisions (i.e., those most influential in leading towards the desired optimum). This focuses human experts' attention on a relatively few decisions and makes them aware of major alternatives. This approach is iterative. Each iteration allows experts to select from among the major alternatives. In successive iterations the execution and summarization modules are run again, but each time further constrained by the decisions made in previous iteration. In the case study shown here, out of 99 yes/no decisions (approximately 10/sup 30/ possibilities), five iterations were sufficient to find and make the 30 key ones.
Sphingomyelin and sphingomyelin synthase (SMS) in the malignant transformation of glioma cells and in 2-hydroxyoleic acid therapy

The mechanism of action of 2-hydroxyoleic acid (2OHOA), a potent antitumor compound, has not yet been fully elucidated. Here, we show that human cancer cells have markedly lower levels of sphingomyelin (SM) than nontumor (MRC-5) cells. In this context, 2OHOA treatment strongly augments SM mass (4.6-fold), restoring the levels found in MRC-5 cells, while a loss of phosphatidylethanolamine and phosphatidylcholine is observed (57 and 30%, respectively). The increased SM mass was due to a rapid and highly specific activation of SM synthases (SMS). This effect appeared to be specific against cancer cells as it did not affect nontumor MRC-5 cells. Therefore, low SM levels are associated with the tumorigenic transformation that produces cancer cells. SM accumulation occurred at the plasma membrane and caused an increase in membrane global order and lipid raft packing in model membranes. These modifications would account for the observed alteration by 2OHOA in the localization of proteins involved in cell apoptosis (Fas receptor) or differentiation (Ras). Importantly, SMS inhibition by D609 diminished 2OHOA effect on cell cycle. Therefore, we propose that the regulation of SMS activity in tumor cells is a critical upstream event in 2OHOA antitumor mechanism, which also explains its specificity for cancer cells, its potency, and the lack of undesired side effects. Finally, the specific activation of SMS explains the ability of this compound to trigger cell cycle arrest, cell differentiation, and autophagy or apoptosis in cancer cells.