On the Modularity of the Intrinsic Flexibility of the μ Opioid Receptor: A Computational Study

The µ opioid receptor (µOR), the principal target to control pain, belongs to the G protein-coupled receptors (GPCRs) family, one of the most highlighted protein families due to their importance as therapeutic targets. The conformational flexibility of GPCRs is one of their essential characteristics as they take part in ligand recognition and subsequent activation or inactivation mechanisms. It is assessed that the intrinsic mechanical properties of the µOR, more specifically its particular flexibility behavior, would facilitate the accomplishment of specific biological functions, at least in their first steps, even in the absence of a ligand or any chemical species usually present in its biological environment. The study of the mechanical properties of the µOR would thus bring some indications regarding the highly efficient ability of the µOR to transduce cellular message. We therefore investigate the intrinsic flexibility of the µOR in its apo-form using all-atom Molecular Dynamics simulations at the sub-microsecond time scale. We particularly consider the µOR embedded in a simplified membrane model without specific ions, particular lipids, such as cholesterol moieties, or any other chemical species that could affect the flexibility of the µOR. Our analyses highlighted an important local effect due to the various bendability of the helices resulting in a diversity of shape and volume sizes adopted by the µOR binding site. Such property explains why the µOR can interact with ligands presenting highly diverse structural geometry. By investigating the topology of the µOR binding site, a conformational global effect is depicted: the correlation between the motional modes of the extra- and intracellular parts of µOR on one hand, along with a clear rigidity of the central µOR domain on the other hand. Our results show how the modularity of the µOR flexibility is related to its pre-ability to activate and to present a basal activity.     

Impacts of Incubation Delay on the Dynamics of an Eco-Epidemiological System—A Theoretical Study

Parasite and predator play significant role in trophic interaction, productivity and stability of an ecosystem. In this paper, we have studied a host-parasite-predator interaction that incorporates incubation delay. How the qualitative and quantitative behaviors of the system alter with the incubation delay have been discussed both from mathematical and biological point of views. It is observed that for a lower infection rate, the system is stable for all delays; but for a higher infection rate, there exists a threshold value of the delay above which the system is unstable and below which the system is stable leading to the persistence of all the species. Also, the instability arising from the incubation delay may be controlled if somehow the growth rate of predator population is increased. Numerical studies have also been performed to illustrate different analytical findings. Research is supported by UGC, India; F No. 32-173/2006(SR).     

Deformation of the Durom Acetabular Component and Its Impact on Tribology in a Cadaveric Model—A Simulator Study

Background

Recent studies have shown that the acetabular component frequently becomes deformed during press-fit insertion. The aim of this study was to explore the deformation of the Durom cup after implantation and to clarify the impact of deformation on wear and ion release of the Durom large head metal-on-metal (MOM) total hips in simulators.

Methods

Six Durom cups impacted into reamed acetabula of fresh cadavers were used as the experimental group and another 6 size-paired intact Durom cups constituted the control group. All 12 Durom MOM total hips were put through a 3 million cycle (MC) wear test in simulators.

Results

The 6 cups in the experimental group were all deformed, with a mean deformation of 41.78±8.86 µm. The average volumetric wear rate in the experimental group and in the control group in the first million cycle was 6.65±0.29 mm³/MC and 0.89±0.04 mm³/MC (t = 48.43, p = 0.000). The ion levels of Cr and Co in the experimental group were also higher than those in the control group before 2.0 MC. However there was no difference in the ion levels between 2.0 and 3.0 MC.

Conclusions

This finding implies that the non-modular acetabular component of Durom total hip prosthesis is likely to become deformed during press-fit insertion, and that the deformation will result in increased volumetric wear and increased ion release.

Clinical Relevance

This study was determined to explore the deformation of the Durom cup after implantation and to clarify the impact of deformation on wear and ion release of the prosthesis. Deformation of the cup after implantation increases the wear of MOM bearings and the resulting ion levels. The clinical use of the Durom large head prosthesis should be with great care.     

Effect of Process Parameters on the Breathing Zone Concentration of Gaseous Hydrocarbons—A Study of an Electrical Discharge Machining Process

The purpose here was to study the effect of process parameters on breathing zone concentrations of gaseous hydrocarbons generated from an Electrical Discharge Machining process. Peak current, pulse duration, dielectric level above the spark location, and flushing pressure were the process parameters considered. Gas chromatography coupled with mass spectrometry (GC/MS) was used to analyze the hydrocarbon components of gaseous emission. Peak current and pulse duration appeared the most significant. A significant fraction of emission was of reaction products of dielectric fluid that included high molecular weight hydrocarbons, branched chain hydrocarbons and other reaction products. Possible measures to control and minimize risk of exposure were outlined as well.     

Impact of Intermittent Apnea on Myocardial Tissue Oxygenation—A Study Using Oxygenation-Sensitive Cardiovascular Magnetic Resonance

Background

Carbon dioxide (CO₂) is a recognized vasodilator of myocardial blood vessels that leads to changes in myocardial oxygenation through the recruitment of the coronary flow reserve. Yet, it is unknown whether changes of carbon dioxide induced by breathing maneuvers can be used to modify coronary blood flow and thus myocardial oxygenation. Oxygenation-sensitive cardiovascular magnetic resonance (CMR) using the blood oxygen level-dependent (BOLD) effect allows for non-invasive monitoring of changes of myocardial tissue oxygenation. We hypothesized that mild hypercapnia induced by long breath-holds leads to changes in myocardial oxygenation that can be detected by oxygenation-sensitive CMR.

Methods and Results

In nine anaesthetized and ventilated pigs, 60s breath-holds were induced. Left ventricular myocardial and blood pool oxygenation changes, as monitored by oxygenation-sensitive CMR using a T2*-weighted steady-state-free-precession (SSFP) sequence at 1.5T, were compared to changes of blood gas levels obtained immediately prior to and after the breath-hold. Long breath-holds resulted in an increase of paCO₂, accompanied by a decrease of paO₂ and pH. There was a significant decrease of blood pressure, while heart rate did not change. A decrease in the left ventricular blood pool oxygenation was observed, which was similar to drop in SaO₂. Oxygenation in the myocardial tissue however, was maintained throughout the period. Changes in myocardial oxygenation were strongly correlated with the change in paCO₂ during the breath-hold (r = 0.90, p = 0.010).

Conclusion

Despite a drop in blood oxygen levels, myocardial oxygenation is maintained throughout long breath-holds and is linearly correlated with the parallel increase of arterial CO₂, a known coronary vasodilator. Breathing maneuvers in combination with oxygenation-sensitive CMR may be useful as a diagnostic test for coronary artery function.     

Effects of Hydroxylated Carbon Nanotubes on the Aggregation of Aβ16–22 Peptides: A Combined Simulation and Experimental Study

The pathogenesis of Alzheimer’s disease (AD) is associated with the aggregation of amyloid-β (Aβ) peptides into toxic aggregates with β-sheet character. In a previous computational study, we showed that pristine single-walled carbon nanotubes (SWCNTs) can inhibit the formation of β-sheet-rich oligomers in the central hydrophobic core fragment of Aβ (Aβ_16–22). However, the poor solubility of SWCNTs in water hinders their use in biomedical applications and nanomedicine. Here, we investigate the influence of hydroxylated SWCNT, a water-soluble SWCNT derivative, on the aggregation of Aβ_16–22 peptides using all-atom explicit-water replica exchange molecular dynamics simulations. Our results show that hydroxylated SWCNTs can significantly inhibit β-sheet formation and shift the conformations of Aβ_16–22 oligomers from ordered β-sheet-rich structures toward disordered coil aggregates. Detailed analyses of the SWCNT-Aβ interaction reveal that the inhibition of β-sheet formation by hydroxylated SWCNTs mainly results from strong electrostatic interactions between the hydroxyl groups of SWCNTs and the positively charged residue K16 of Aβ_16–22 and hydrophobic and aromatic stacking interactions between SWCNTs and F19 and F20. In addition, our atomic force microscopy and thioflavin T fluorescence experiments confirm the inhibitory effect of both pristine and hydroxylated SWCNTs on Aβ_16–22 fibrillization, in support of our previous and present replica exchange molecular dynamics simulation results. These results demonstrate that hydroxylated SWCNTs efficiently inhibit the aggregation of Aβ_16–22; in addition, they offer molecular insight into the inhibition mechanism, thus providing new clues for the design of therapeutic drugs against amyloidosis.     

AlphaFold – A Personal Perspective on the Impact of Machine Learning

I outline how over my career as a protein scientist Machine Learning has impacted my area of science and one of my pastimes, chess, where there are some interesting parallels. In 1968, modelling of three-dimensional structures was initiated based on a known structure as a template, the problem of the pathway of protein folding was posed and bets were taken in the emerging field of Machine Learning on whether computers could outplay humans at chess. Half a century later, Machine Learning has progressed from using computational power combined with human knowledge in solving problems to playing chess without human knowledge being used, where it has produced novel strategies. Protein structures are being solved by Machine Learning based on human-derived knowledge but without templates. There is much promise that programs like AlphaFold based on Machine Learning will be powerful tools for designing entirely novel protein folds and new activities. But, will they produce novel ideas on protein folding pathways and provide new insights into the principles that govern folds?     

Impact of Withholding Breastfeeding at the Time of Vaccination on the Immunogenicity of Oral Rotavirus Vaccine—A Randomized Trial

BackgroundBreast milk contains anti-rotavirus IgA antibodies and other innate immune factors that inhibit rotavirus replication in vitro. These factors could diminish the immunogenicity of oral rotavirus vaccines, particularly if breastfeeding occurs close to the time of vaccine administration.MethodsBetween April 2011 and November 2012, we conducted an open label, randomized trial to compare the immunogenicity of Rotarix (RV1) in infants whose breastfeeding was withheld one hour before through one hour after vaccination with that in infants breastfed at the time of vaccination. The trial was conducted in the peri-urban area of Ibrahim Hyderi in Karachi, Pakistan. Both groups received three doses of RV1 at 6, 10 and 14 weeks of age. Seroconversion (anti-rotavirus IgA antibodies ≥20 U/mL in subjects seronegative at 6 weeks of age) following three vaccine doses (6, 10 and 14 weeks) was determined at 18 weeks of age (primary objective) and seroconversion following two doses (6 and 10 weeks) was determined at 14 weeks of age (secondary objective).ResultsFour hundred eligible infants were randomly assigned in a 1:1 ratio between the withholding breastfeeding and immediate breastfeeding arms. Overall, 353 (88.3%) infants completed the study according to protocol; 181 in the withholding breastfeeding group and 172 in the immediate breastfeeding group. After three RV1 doses, anti-rotavirus IgA antibody seroconversion was 28.2% (95% CI: 22.1; 35.1) in the withholding arm and 37.8% (95% CI: 30.9; 45.2) in the immediate breastfeeding arm (difference: -9.6% [95% CI: -19.2; 0.2] p=0.07). After two doses of RV1, seroconversion was 16.6% (95% CI: 11.9; 22.7) in the withholding arm and 29.1% (95% CI: 22.8, 36.3) in the immediate breastfeeding arm (difference: -12.5% [95% CI: -21.2,-3.8] p=0.005).ConclusionsWithholding breastfeeding around the time of RV1 vaccine administration did not lead to increased anti-rotavirus IgA seroconversion compared with that seen with a breastfeed at the time of vaccination. On the contrary, IgA seroconversion in infants immediately breastfed tended to be higher than in those withheld from a feeding. Our findings suggest that breastfeeding should be continued adlib around the time of rotavirus vaccination and withholding breastfeeding at that time is unlikely to improve the vaccine immunogenicity.

Trial Registration

ClinicalTrials.gov NCT01199874     

Evaluation of the Septifast MGrade Test on Standard Care Wards—A Cohort Study

Background

The immediate need for appropriate antimicrobial therapy in septic patients requires the detection of the causative pathogen in a timely and reliable manner. In this study, the real-time PCR Septifast M^Grade test was evaluated in adult patients meeting the systemic inflammatory response syndrome (SIRS) criteria that were treated at standard care wards.

Methods

Patients with clinical suspected infection, drawn blood cultures (BC), the Septifast M^Grade test (SF) and sepsis biomarkers were prospectively screened for fulfillment of SIRS criteria and evaluated using the criteria of the European Centre of Disease Control (ECDC) for infection point prevalence studies.

Results

In total, 220 patients with SIRS were prospectively enrolled, including 56 patients with detection of bacteria in the blood (incidence: 25.5%). BC analysis resulted in 75.0% sensitivity (95% confidence interval, CI: 61.6%– 85.6%) with 97.6% specificity (CI: 93.9%– 99.3%) for detecting bacteria in the blood. In comparison to BC, SF presented with 80.4% sensitivity (CI: 67.6%– 89.8%) and with 97.6% specificity (CI: 93.9%– 99.3%). BC and SF analysis yielded comparable ROC-AUCs (0.86, 0.89), which did not differ significantly (p = 0.558). A trend of a shorter time-to-positivity of BC analysis was not seen in bacteremic patients with a positive SF test than those with a negative test result. Sepsis biomarkers, including PCT, IL-6 or CRP, did not help to explain discordant test results for BC and SF.

Conclusion

Since negative results do not exclude bacteremia, the Septifast M^Grade test is not suited to replacing BC, but it is a valuable tool with which to complement BC for faster detection of pathogens.     

Could CCI or FBCI Fully Eliminate the Impact of Curve Flexibility When Evaluating the Surgery Outcome for Thoracic Curve Idiopathic Scoliosis Patient? A Retrospective Study

PurposeTo clarify if CCI or FBCI could fully eliminate the influence of curve flexibility on the coronal correction rate.MethodsWe reviewed medical record of all thoracic curve AIS cases undergoing posterior spinal fusion with all pedicle screw systems from June 2011 to July 2013. Radiographical data was collected and calculated. Student t test, Pearson correlation analysis and linear regression analysis were used to analyze the data.Results60 were included in this study. The mean age was 14.7y (10-18y) with 10 males (17%) and 50 females (83%). The average Risser sign was 2.7. The mean thoracic Cobb angle before operation was 51.9°. The mean bending Cobb angle was 27.6° and the mean fulcrum bending Cobb angle was 17.4°. The mean Cobb angle at 2 week after surgery was 16.3°. The Pearson correlation coefficient r between CCI and BFR was -0.856(P<0.001), and between FBCI and FFR was -0.728 (P<0.001). A modified FBCI (M-FBCI) = (CR-0.513)/BFR or a modified CCI (M-CCI) = (CR-0.279)/FFR was generated by curve estimation has no significant correlation with FFR (r=-0.08, p=0.950) or with BFR (r=0.123, p=0.349).ConclusionsFulcrum-bending radiographs may better predict the outcome of AIS coronal correction than bending radiographs in thoracic curveAIS patients. Neither CCI nor FBCI can fully eliminate the impact of curve flexibility on the outcome of correction. A modified CCI or FBCI can better evaluating the corrective effects of different surgical techniques or instruments.     

On the Origin of Rheumatoid Arthritis: The Impact of Environment and Genes—A Population Based Twin Study

Background

Rheumatoid arthritis (RA) is an autoimmune disease with a complex origin. Previous studies have reported heritability estimates on RA at about 60%. Only 16% of the genetic background of the disease has been disclosed so far. The purpose of the present investigation was to provide an optimized estimate on the heritability of RA and to study the recurrence risk in a nationwide Caucasian twin population.

Methods and Findings

In a mail survey addressed to 56.707 twin individuals, RA was reported by 479 individuals, mean age 52 (range 16–73). Respondents underwent an interview and clinical examination. Ascertainment probability was 80%. RA was confirmed in 162 twin individuals yielding a prevalence at 0.37% (95% CI 0.31–0.43). The mean discordance time was 19 years (range 0–57). The concordance was 9.1% (95% CI 1.9 to 24.3) in MZ, 6.4% (95% CI 2.1 to 14.3) in DZss. The increased relative risk of attracting RA conditioned on having an affected cotwin compared to the background population risk was 24.6 to 35.4 in MZ twins and 17.3 to 31.6 in DZss twins. The correlation coefficients were 0.60 (0.33 to 0.78) in monozygotic (MZ) and 0.55 (0.33 to 0.72) in dizygotic same sexed (DZss) pairs. Twelve percent (95% CI 0–76%) of the phenotypic variance in the liability to RA was due to additive genetic effects, 50% (95% CI 0–72%) to shared environmental effects and 38% (95% CI 17–61%) to non-shared environmental effects.

Conclusions

This study emphasizes that family factors are important for the development of RA. Although genetic effectors are important, shared and non-shared environmental triggers and/or epigenetic stochastic events seem to be even more significant. However, it should be borne in mind that the genetic and non-genetic components may not be the same across disease subsets.     

Lubricating Properties of the Initial Salivary Pellicle — an AFM Study

The role of saliva in the oral cavity is manifold; an important function is to serve as lubricant between hard (enamel) and soft (mucosal) tissues. Intraoral lubrication is of crucial importance in order to maintain functions such as deglutition, mastication and the faculty of speech. A large number of people suffer from impaired salivary functions, displaying symptoms such as ‘dry mouth’. This results in a need for methods to assess the lubricating properties of both native saliva and potential artificial saliva formulations. Here, normal as well as lateral forces, acting between adsorbed salivary films, have been measured for the first time by means of colloidal probe atomic force microscopy (AFM). It was found that the presence of salivary pellicles between hard surfaces reduces the friction coefficient by a factor of 20. This reduction of friction is consistent with the long-range purely repulsive nature of the normal forces acting between the salivary films. The lubricating mechanism is presumably based on a full separation of the sliding surfaces by the salivary films. The friction between salivary films has been investigated at normal loads that cover the clinical jaw closing forces, and it can be concluded that the lubricating properties are maintained within this load interval. The present study indicates the usefulness of colloidal probe AFM, which offers a direct and quantitative measure of lubrication at a molecular level, in the study of biotribological phenomena. In particular, the results obtained here may have implications for the development of saliva substitutes.     

A Study on In-Line Tablet Coating—the Influence of Compaction and Coating on Tablet Dimensional Changes

Prior to coating, tablets are usually stored for a definite period to enable complete strain recovery and prevent subsequent volumetric expansion-related coating defects. In-line coating is defined as the coating of tablets immediately after compaction. In-line coating will be expected to improve manufacturing efficiencies. In this study, the possibility of in-line coating was studied by evaluating the influence of compaction and coating on tablet dimensional changes. The use of tapered dies for compaction was also evaluated. Two types of tablet coaters which presented different coating environments, namely the Supercell™ coater and pan coater, were employed for coating. The extent of tablet dimensional changes was studied in real time using optical laser sensors in a controlled environment. After compaction, tablet dimensional changes were found to be anisotropic. In contrast, coating resulted in isotropic volume expansion in both the axial and radial directions. Pan coating resulted in significantly greater tablet dimensional changes compared to Supercell™ coating. There was no significant difference in dimensional changes of tablets coated in line or after complete viscoelastic strain recovery for Supercell™ coating. However, significantly different dimensional changes were observed for pan coating. The use of tapered dies during compaction was found to result in more rapid viscoelastic strain recovery and also significantly reduced tablet dimensional changes when tablets were immediately coated after compaction using the pan coater. In conclusion, the Supercell™ coater appeared to be more suitable for in-line tablet coating, while tapered dies were beneficial in reducing tablet dimensional changes when the pan coater was employed for in-line coating.KEY WORDS: continuous manufacturing, in-line coating, tablet coating, tapered dies, viscoelastic strain recovery     

Enhancement and Entitlement—the Impact of Stocking on Rural Households’ Command over Living Aquatic Resources: A Case Study from the Lao PDR

Enhancement of inland fisheries through stocking can potentially increase fisheries production in developing countries and improve rural livelihoods. However, results of stocking are often unexpected in terms of benefit distribution. Taking an environmental entitlements approach, this paper details the nature and extent of institutional change that accompanied stocking in Savannakhet Province, Lao PDR, and quantifies its impact on households from different socioeconomic groups. Stocking was a catalyst significantly affecting people’s command over living aquatic resources. New rules changed who could go fishing for what and when, and how the fish could be utilized. Customary rights were transformed and decision-making power concentrated. Despite this, household surveys demonstrated that no socioeconomic group was benefiting disproportionately and this was due to the specific social, political and institutional context into which enhancement was placed. However, in different contexts, increased benefits for resource users, even in cases of increased fisheries production, cannot be assumed.

Simulation Study of the Effect of Surface Plasmon Coupling on Förster Resonance Energy Transfer Behavior

Plasmonics - The effect of surface plasmon (SP) coupling of an Ag sphere on the behavior of the Förster resonance energy transfer (FRET) from a donor dipole into an acceptor nearby is...     

A Lipidomic Study of the Effects of N-methyl-N＇-nitro-N-nitrosoguanidine on Sphingomyelin Metabolism

Systems biology is a new and rapidly developing research area in which, by quantitatively describing the interaction among all the individual components of a cell, a systems-level understanding of a biological response can be achieved. Therefore, it requires high-throughput measurement technologies for biological molecules, such as genomic and proteomic approaches for DNA/RNA and protein, respectively.Recently, a new concept, lipidomics, which utilizes the mass spectrometry （MS） method for lipid analysis,has been proposed. Using this lipidomic approach, the effects of N-methyl-N＇-nitro-N-nitrosoguanidine （MNNG） on sphingomyelin metabolism, a major class of sphingolipids, were evaluated. Sphingomyelin molecules were extracted from cells and analyzed by matrix-assisted laser desorption ionization-time of flight MS. It was found that MNNG induced profound changes in sphingomyelin metabolism, including the appearance of some new sphingomyelin species and the disappearance of some others, and the concentrations of several sphingomyelin species also changed. This was accompanied by the redistribution of acid sphingomyelinase （ASM）, a key player in sphingomyelin metabolism. On the other hand, imipramine, an inhibitor of ASM,caused the accumulation of sphingomyelin. It also prevented some of the effects of MNNG, as well as the redistribution of ASM. Taken together, these data suggested that the lipidomic approach is highly effective for the systematic analysis of cellular lipids metabolism.     

A Lipidomic Study of the Effects of N-methyl-N′-nitro-N-nitrosoguanidine on Sphingomyelin Metabolism

Systems biology is a new and rapidly developing research area in which,by quantitativelydescribing the interaction among all the individual components of a cell,a systems-level understanding of abiological response can be achieved.Therefore,it requires high-throughput measurement technologies forbiological molecules,such as genomic and proteomic approaches for DNA/RNA and protein,respectively.Recently,a new concept,lipidomics,which utilizes the mass spectrometry(MS)method for lipid analysis,has been proposed.Using this lipidomic approach,the effects of N-methyl-N'-nitro-N-nitrosoguanidine(MNNG)on sphingomyelin metabolism,a major class of sphingolipids,were evaluated.Sphingomyelin moleculeswere extracted from cells and analyzed by matrix-assisted laser desorption ionization-time of flight MS.Itwas found that MNNG induced profound changes in sphingomyelin metabolism,including the appearance ofsome new sphingomyelin species and the disappearance of some others,and the concentrations of severalsphmgomyelin species also changed.This was accompanied by the redistribution of acid sphingomyelinase(ASM),a key player in sphingomyelin metabolism.On the other hand,imipramine,an inhibitor of ASM,caused the accumulation of sphingomyelin.It also prevented some of the effects of MNNG,as well as theredistribution of ASM.Taken together,these data suggested that the lipidomic approach is highly effectivefor the systematic analysis of cellular lipids metabolism.