Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?

Computational chemistry is an important tool in numerous scientific disciplines, including drug discovery and structural biology. Coarse-grained models offer simple representations of molecular systems that enable simulations of large-scale systems. Because there has been an increase in the adoption of such models for simulations of biomolecular systems, critical evaluation is warranted. Here, the stability of the amyloid peptide and organic crystals is evaluated using the Martini 3 coarse-grained force field. The crystals change shape drastically during the simulations. Radial distribution functions show that the distance between backbone beads in β-sheets increases by ∼1 Å, breaking the crystals. The melting points of organic compounds are much too low in the Martini force field. This suggests that Martini 3 lacks the specific interactions needed to accurately simulate peptides or organic crystals without imposing artificial restraints. The problems may be exacerbated by the use of the 12-6 potential, suggesting that a softer potential could improve this model for crystal simulations.

Quantitative Predictions of the Thermal Conductivity in Transition Metal Dichalcogenides: Impact of Point Defects in MoS2 and WS2 Monolayers

Transition metal dichalcogenides are investigated for various applications at the nanoscale because of their unique combination of properties and dimensionality. For many of the anticipated applications, heat conduction plays an important role. At the same time, these materials often contain relatively large amounts of point defects. Here, we provide a systematic analysis of the impact of intrinsic and selected extrinsic defects on the lattice thermal conductivity of MoS2 and WS2 monolayers. We combine Boltzmann transport theory and Green's function-based T-matrix approach for the calculation of scattering rates. The force constants for the defect configurations are obtained from density functional theory calculations via a regression approach, which allows us to sample a rather large number of defects at a moderate computational cost and to systematically enforce both the translational and rotational acoustic sum rules. The calculated lattice thermal conductivity is in quantitative agreement with the experimental data for heat transport and defect concentrations for both MoS2 and WS2. Crucially, this demonstrates that the strong deviation from a 1/T temperature dependence of the lattice thermal conductivity observed experimentally can be fully explained by the presence of point defects. We furthermore predict the scattering strengths of the intrinsic defects to decrease in the sequence VMo ≈ V2S= > V2S⊥ > VS > Sad in both materials, while the scattering rates for the extrinsic (adatom) defects decrease with increasing mass such that Liad > Naad > Kad. Compared with earlier work, we find that both intrinsic and extrinsic adatoms are relatively weak scatterers. We attribute this difference to the treatment of the translational and rotational acoustic sum rules, which, if not enforced, can lead to spurious contributions in the zero-frequency limit.

Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation

In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.

Simulations of the Aqueous "Brown-Ring" Complex Reveal Fluctuations in Electronic Character

Ab initio molecular dynamics (AIMD) simulations of the aqueous [Fe(H2O)5(NO)]2+ "brown-ring" complex in different spin states, in combination with multiconfigurational quantum chemical calculations, show a structural dependence on the electronic character of the complex. Sampling in the quartet and sextet ground states show that the multiplicity is correlated with the Fe-N distance. This provides a motivation for a rigid Fe-N scan in the isolated "brown-ring" complex to investigate how the multiconfigurational wave function and the electron density change around the FeNO moiety. Our results show that subtle changes in the Fe-N distance produce a large response in the electronic configurations underlying the quartet wave function. However, while changes in spin density and potential energy are pronounced, variations in charge are negligible. These trends within the FeNO moiety are preserved in structural sampling of the AIMD simulations, despite distortions present in other degrees of freedom in the bulk solution.

Development of a dynamic interactive web tool to enhance understanding of multi-state model analyses: MSMplus

BACKGROUND

Multi-state models are used in complex disease pathways to describe a process where an individual moves from one state to the next, taking into account competing states during each transition. In a multi-state setting, there are various measures to be estimated that are of great epidemiological importance. However, increased complexity of the multi-state setting and predictions over time for individuals with different covariate patterns may lead to increased difficulty in communicating the estimated measures. The need for easy and meaningful communication of the analysis results motivated the development of a web tool to address these issues.

RESULTS

MSMplus is a publicly available web tool, developed via the Shiny R package, with the aim of enhancing the understanding of multi-state model analyses results. The results from any multi-state model analysis are uploaded to the application in a pre-specified format. Through a variety of user-tailored interactive graphs, the application contributes to an improvement in communication, reporting and interpretation of multi-state analysis results as well as comparison between different approaches. The predicted measures that can be supported by MSMplus include, among others, the transition probabilities, the transition intensity rates, the length of stay in each state, the probability of ever visiting a state and user defined measures. Representation of differences, ratios and confidence intervals of the aforementioned measures are also supported. MSMplus is a useful tool that enhances communication and understanding of multi-state model analyses results.

CONCLUSIONS

Further use and development of web tools should be encouraged in the future as a means to communicate scientific research.

Permafrost Thaw Increases Methylmercury Formation in Subarctic Fennoscandia

Methylmercury (MeHg) forms in anoxic environments and can bioaccumulate and biomagnify in aquatic food webs to concentrations of concern for human and wildlife health. Mercury (Hg) pollution in the Arctic environment may worsen as these areas warm and Hg, currently locked in permafrost soils, is remobilized. One of the main concerns is the development of Hg methylation hotspots in the terrestrial environment due to thermokarst formation. The extent to which net methylation of Hg is enhanced upon thaw is, however, largely unknown. Here, we have studied the formation of Hg methylation hotspots using existing thaw gradients at five Fennoscandian permafrost peatland sites. Total Hg (HgT) and MeHg concentrations were analyzed in 178 soil samples from 14 peat cores. We observed 10 times higher concentrations of MeHg and 13 times higher %MeHg in the collapse fen (representing thawed conditions) as compared to the peat plateau (representing frozen conditions). This suggests significantly greater net methylation of Hg when thermokarst wetlands are formed. In addition, we report HgT to soil organic carbon ratios representative of Fennoscandian permafrost peatlands (median and interquartile range of 0.09 ± 0.07 μg HgT g^-1 C) that are of value for future estimates of circumpolar HgT stocks.

Direct modelling of age standardized marginal relative survival through incorporation of time-dependent weights

BACKGROUND

When quantifying the probability of survival in cancer patients using cancer registration data, it is common to estimate marginal relative survival, which under assumptions can be interpreted as marginal net survival. Net survival is a hypothetical construct giving the probability of being alive if it was only possible to die of the cancer under study, enabling comparisons between populations with differential mortality rates due to causes other the cancer under study. Marginal relative survival can be estimated non-parametrically (Pohar Perme estimator) or in a modeling framework. In a modeling framework, even when just interested in marginal relative survival it is necessary to model covariates that affect the expected mortality rates (e.g. age, sex and calendar year). The marginal relative survival function is then obtained through regression standardization. Given that these covariates will generally have non-proportional effects, the model can become complex before other exposure variables are even considered.

METHODS

We propose a flexible parametric model incorporating restricted cubic splines that directly estimates marginal relative survival and thus removes the need to model covariates that affect the expected mortality rates. In order to do this the likelihood needs to incorporate the marginal expected mortality rates at each event time taking account of informative censoring. In addition time-dependent weights are incorporated into the likelihood. An approximation is proposed through splitting the time scale into intervals, which enables the marginal relative survival model to be fitted using standard software. Additional weights can be incorporated when standardizing to an external reference population.

RESULTS

The methods are illustrated using national cancer registry data. In addition, a simulation study is performed to compare different estimators; a non-parametric approach, regression-standardization and the new marginal relative model. The simulations study shows the new approach is unbiased and has good relative precision compared to the non-parametric estimator.

CONCLUSION

The approach enables estimation of standardized marginal relative survival without the need to model covariates that affect expected mortality rates and thus reduces the chance of model misspecification.

Extensive undertreatment of osteoporosis in older Swedish women

In a population-based study of older Swedish women, we investigated the proportion of women treated with osteoporosis medication in relation to the proportion of women eligible for treatment according to national guidelines. We found that only a minority (22%) of those eligible for treatment were prescribed osteoporosis medication.

INTRODUCTION

Fracture rates increase markedly in old age and the incidence of hip fracture in Swedish women is among the highest in the world. Although effective pharmacological treatment is available, treatment rates remain low. Limited data are available regarding treatment rates in relation to fracture risk in a population-based setting in older women. Therefore, we aimed to investigate the proportion of older women eligible for treatment according to Swedish Osteoporosis Society (SvOS) guidelines.

METHODS

A population-based study was performed in Gothenburg in 3028 older women (77.8 ± 1.6 years [mean ± SD]). Bone mineral density of the spine and hip was measured with dual-energy X-ray absorptiometry. Clinical risk factors for fracture and data regarding osteoporosis medication was collected with self-administered questionnaires. Logistic regression was used to evaluate whether the 10-year probability of sustaining a major osteoporotic fracture (FRAX-score) or its components predicted treatment with osteoporosis medication.

RESULTS

For the 2983 women with complete data, 1107 (37%) women were eligible for treatment using SvOS criteria. The proportion of these women receiving treatment was 21.8%. For women eligible for treatment according to SvOS guidelines, strong predictors for receiving osteoporosis medication were glucocorticoid treatment (odds ratio (95% CI) 2.88 (1.80-4.59)) and prior fracture (2.58 (1.84-3.61)).

CONCLUSION

This study demonstrates that a substantial proportion of older Swedish women should be considered for osteoporosis medication given their high fracture risk, but that only a minority receives treatment.

Can markers of biological age predict dependency in old age?

Recent research has shown that markers of biological age, such as leukocyte telomere length (LTL), epigenetic clocks and the frailty index (FI) are predictive of mortality and age-related diseases. However, whether these markers associate with the need for care in old age, thereby having utility in reflecting dependency, is unclear. This study was undertaken to analyze whether LTL, two epigenetic clocks-the DNA methylation age (DNAmAge) and DNAm PhenoAge-and the FI are associated with the need for regular care in up to 604 individuals (aged 48-94 years) participating in the Swedish Adoption/Twin Study of Aging. Need for regular care was defined as receiving formal or informal help in daily routines at least once per week. Logistic regression adjusted for age, sex and education was used in the analysis. The predictive accuracies, assessed as the area under the curve (AUC) for the significant biological age measures were further compared to the accuracies of the limitations in activities of daily living (ADL) and instrumental ADL (IADL). Neither LTL nor the epigenetic clocks were associated with the need for care, whereas the FI was; odds ratio for 10% increase in FI 3.54 (95% confidence interval 2.32-5.41). The FI also demonstrated higher predictive accuracy than the ADL score (FI AUC 0.80 vs. ADL score AUC 0.62; p < 0.001 for equality of the AUCs), whereas the difference between FI AUC (0.80) and IADL score AUC (0.75) was not significant (p = 0.238). The FI might thus be a useful marker for the need for care.

Epidemiology of osteonecrosis among older adults in Sweden

This study estimated the incidence of osteonecrosis in a Swedish, nationwide cohort of older adults. Osteonecrosis was approximately 10 times more common than in previous studies. The strongest risk factors were dialysis, hip fracture, osteomyelitis, and organ transplantation, but only hip fractures could have contributed substantially to the disease burden.

INTRODUCTION

The aim of this study was to estimate the incidence of osteonecrosis in a Swedish, nationwide cohort of older adults and in a large number of risk groups in that cohort.

METHODS

In this retrospective cohort study, we included everyone who was aged 50 years or older and who was living in Sweden on 31 December 2005. We used Swedish national databases to collect data about prescription medication use, diagnosed medical conditions, and performed medical and surgical procedures. The study outcome was diagnosis of primary or secondary osteonecrosis at any skeletal site. The strength of risk factors was assessed using age- and sex-standardized incidence ratios (SIRs).

RESULTS

The study cohort comprised 3,338,463 adults. The 10-year risk of osteonecrosis was 0.4% (n = 13,425), and the incidence rate was 4.7 cases/10000 person-years (95% confidence interval [CI], 4.6 to 4.7 cases). The strongest risk factors for osteonecrosis were hip fracture (SIR, 7.98; 95% CI, 7.69-8.27), solid organ transplantation (SIR, 7.14; 95% CI, 5.59-8.99), dialysis (SIR, 6.65; 95% CI, 5.62-7.81), and osteomyelitis (SIR, 6.43; 95% CI, 5.70-7.23). A history of hip fracture was present in 21.7% of cases of osteonecrosis, but osteomyelitis, dialysis, and solid organ transplantation were present in only 0.5 to 2% of cases.

CONCLUSIONS

Osteonecrosis was approximately 10 times more common than a small number of previous population-based studies have suggested. The strongest risk factors for osteonecrosis were dialysis, hip fracture, osteomyelitis, and solid organ transplantation, but only hip fractures could have contributed substantially to the disease burden.

Pridopidine Induces Functional Neurorestoration Via the Sigma-1 Receptor in a Mouse Model of Parkinson's Disease

Pridopidine is a small molecule in clinical development for the treatment of Huntington's disease. It was recently found to have high binding affinity to the sigma-1 receptor, a chaperone protein involved in cellular defense mechanisms and neuroplasticity. Here, we have evaluated the neuroprotective and neurorestorative effects of pridopidine in a unilateral 6-hydroxydopamine (6-OHDA) lesion model of parkinsonism in mice. By 5 weeks of daily administration, a low dose of pridopidine (0.3 mg/kg) had significantly improved deficits in forelimb use (cylinder test, stepping test) and abolished the ipsilateral rotational bias typical of hemiparkinsonian animals. A higher dose of pridopidine (1 mg/kg) significantly improved only the rotational bias, with a trend towards improvement in forelimb use. The behavioral recovery induced by pridopidine 0.3 mg/kg was accompanied by a significant protection of nigral dopamine cell bodies, an increased dopaminergic fiber density in the striatum, and striatal upregulation of GDNF, BDNF, and phosphorylated ERK1/2. The beneficial effects of pridopidine 0.3 mg/kg were absent in 6-OHDA-lesioned mice lacking the sigma-1 receptor. Pharmacokinetic data confirmed that the effective dose of pridopidine reached brain concentrations sufficient to bind S1R. Our results are the first to show that pridopidine promotes functional neurorestoration in the damaged nigrostriatal system acting via the sigma-1 receptor.

Targeted Oligonucleotides for Treating Neurodegenerative Tandem Repeat Diseases

Nucleotide repeat disorders encompass more than 30 diseases, most of which show dominant inheritance, such as Huntington's disease, spinocerebellar ataxias, and myotonic dystrophies. Yet others, including Friedreich's ataxia, are recessively inherited. A common feature is the presence of a DNA tandem repeat in the disease-associated gene and the propensity of the repeats to expand in germ and in somatic cells, with ensuing neurological and frequently also neuromuscular defects. Repeat expansion is the most frequent event in these diseases; however, sequence contractions, deletions, and mutations have also been reported. Nucleotide repeat sequences are predisposed to adopt non-B-DNA conformations, such as hairpins, cruciform, and intramolecular triple-helix structures (triplexes), also known as H-DNA. For gain-of-function disorders, oligonucleotides can be used to target either transcripts or duplex DNA and in diseases with recessive inheritance oligonucleotides may be used to alter repressive DNA or RNA conformations. Most current treatment strategies are aimed at altering transcript levels, but therapies directed against DNA are also emerging, and novel strategies targeting DNA, instead of RNA, are described. Different mechanisms using modified oligonucleotides are discussed along with the structural aspects of repeat sequences, which can influence binding modes and efficiencies.