Why do eukaryotic proteins contain more intrinsically disordered regions?

Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins. Methods predicting intrinsic disorder are based on the amino acid sequence of a protein. Therefore, there must exist an underlying difference in the sequences between eukaryotic and prokaryotic proteins causing the (predicted) difference in intrinsic disorder. By comparing proteins, from complete eukaryotic and prokaryotic proteomes, we show that the difference in intrinsic disorder emerges from the linker regions connecting Pfam domains. Eukaryotic proteins have more extended linker regions, and in addition, the eukaryotic linkers are significantly more disordered, 38% vs. 12-16% disordered residues. Next, we examined the underlying reason for the increase in disorder in eukaryotic linkers, and we found that the changes in abundance of only three amino acids cause the increase. Eukaryotic proteins contain 8.6% serine; while prokaryotic proteins have 6.5%, eukaryotic proteins also contain 5.4% proline and 5.3% isoleucine compared with 4.0% proline and ≈ 7.5% isoleucine in the prokaryotes. All these three differences contribute to the increased disorder in eukaryotic proteins. It is tempting to speculate that the increase in serine frequencies in eukaryotes is related to regulation by kinases, but direct evidence for this is lacking. The differences are observed in all phyla, protein families, structural regions and type of protein but are most pronounced in disordered and linker regions. The observation that differences in the abundance of three amino acids cause the difference in disorder between eukaryotic and prokaryotic proteins raises the question: Are amino acid frequencies different in eukaryotic linkers because the linkers are more disordered or do the differences cause the increased disorder?

Intrinsic disorder is essential for various functions in eukaryotic cells and is a signature of eukaryotic proteins. Here, we try to understand the origin of the difference in disorder between eukaryotic and prokaryotic proteins. We show that eukaryotic proteins contain more extended linker regions and that these linker regions are significantly more disordered. Further, we show, for the first time, that the difference in disorder originates from a systematic difference in amino acid frequencies between eukaryotic and prokaryotic proteins. Three amino acids contribute to the difference in disorder; serine and proline are more abundant in eukaryotic linkers, while isoleucine is less frequent. These shifts in frequencies are observed in all phyla, protein families, structural regions and type of protein but are most pronounced in disordered and linker regions. It is tempting to speculate that the increase in serine frequencies in eukaryotes is related to regulation by kinases, but direct evidence for this is lacking. Anyhow the widespread of the shifts in abundance indicates that the differences are ancient and caused be some yet not fully understood selective difference acting on eukaryotic and prokaryotic proteins.

Model-inferred mechanisms of liver function from magnetic resonance imaging data: Validation and variation across a clinically relevant cohort

Estimation of liver function is important to monitor progression of chronic liver disease (CLD). A promising method is magnetic resonance imaging (MRI) combined with gadoxetate, a liver-specific contrast agent. For this method, we have previously developed a model for an average healthy human. Herein, we extended this model, by combining it with a patient-specific non-linear mixed-effects modeling framework. We validated the model by recruiting 100 patients with CLD of varying severity and etiologies. The model explained all MRI data and adequately predicted both timepoints saved for validation and gadoxetate concentrations in both plasma and biopsies. The validated model provides a new and deeper look into how the mechanisms of liver function vary across a wide variety of liver diseases. The basic mechanisms remain the same, but increasing fibrosis reduces uptake and increases excretion of gadoxetate. These mechanisms are shared across many liver functions and can now be estimated from standard clinical images.

Being able to accurately and reliably estimate liver function is important when monitoring the progression of patients with liver disease, as well as when identifying drug-induced liver injury during drug development. A promising method for quantifying liver function is to use magnetic resonance imaging combined with gadoxetate. Gadoxetate is a liver-specific contrast agent, which is taken up by the hepatocytes and excreted into the bile. We have previously developed a mechanistic model for gadoxetate dynamics using averaged data from healthy volunteers. In this work, we extended our model with a non-linear mixed-effects modeling framework to give patient-specific estimates of the gadoxetate transport-rates. We validated the model by recruiting 100 patients with liver disease, covering a range of severity and etiologies. All patients underwent an MRI-examination and provided both blood and liver biopsies. Our validated model provides a new and deeper look into how the mechanisms of liver function varies across a wide variety of liver diseases. The basic mechanisms remain the same, but increasing fibrosis reduces uptake and increases excretion of gadoxetate.

Prevalence of intimate partner violence against women in Sweden and Spain: A psychometric study of the 'Nordic paradox'

The high prevalence of intimate partner violence against women (IPVAW) in countries with high levels of gender equality has been defined as the “Nordic paradox”. In this study we compared physical and sexual IPVAW prevalence data in two countries exemplifying the Nordic paradox: Sweden (N = 1483) and Spain (N = 1447). Data was drawn from the European Union Agency for Fundamental Rights Survey on violence against women. To ascertain whether differences between these two countries reflect true differences in IPVAW prevalence, and to rule out the possibility of measurement bias, we conducted a set of analyses to ensure measurement equivalence, a precondition for appropriate and valid cross-cultural comparisons. Results showed that in both countries items were measuring two separate constructs, physical and sexual IPVAW, and that these factors had high internal consistency and adequate validity. Measurement equivalence analyses (i.e., differential item functioning, and multigroup confirmatory factor analysis) supported the comparability of data across countries. Latent means comparisons between the Spanish and the Swedish samples showed that scores on both the physical and sexual IPVAW factors were significantly higher in Sweden than in Spain. The effect sizes of these differences were large: 89.1% of the Swedish sample had higher values in the physical IPVAW factor than the Spanish average, and this percentage was 99.4% for the sexual IPVAW factor as compared to the Spanish average. In terms of probability of superiority, there was an 80.7% and 96.1% probability that a Swedish woman would score higher than a Spanish woman in the physical and the sexual IPVAW factors, respectively. Our results showed that the higher prevalence of physical and sexual IPVAW in Sweden than in Spain reflects actual differences and are not the result of measurement bias, supporting the idea of the Nordic paradox.

A natural history model for planning prostate cancer testing: Calibration and validation using Swedish registry data

Recent prostate cancer screening trials have given conflicting results and it is unclear how to reduce prostate cancer mortality while minimising overdiagnosis and overtreatment. Prostate cancer testing is a partially observable process, and planning for testing requires either extrapolation from randomised controlled trials or, more flexibly, modelling of the cancer natural history. An existing US prostate cancer natural history model (Gulati et al, Biostatistics 2010;11:707-719) did not model for differences in survival between Gleason 6 and 7 cancers and predicted too few Gleason 7 cancers for contemporary Sweden. We re-implemented and re-calibrated the US model to Sweden. We extended the model to more finely describe the disease states, their time to biopsy-detectable cancer and prostate cancer survival. We first calibrated the model to the incidence rate ratio observed in the European Randomised Study of Screening for Prostate Cancer (ERSPC) together with age-specific cancer staging observed in the Stockholm PSA (prostate-specific antigen) and Biopsy Register; we then calibrated age-specific survival by disease states under contemporary testing and treatment using the Swedish National Prostate Cancer Register. After calibration, we were able to closely match observed prostate cancer incidence trends in Sweden. Assuming that patients detected at an earlier stage by screening receive a commensurate survival improvement, we find that the calibrated model replicates the observed mortality reduction in a simulation of ERSPC. Using the resulting model, we predicted incidence and mortality following the introduction of regular testing. Compared with a model of the current testing pattern, organised 8 yearly testing for men aged 55–69 years was predicted to reduce prostate cancer incidence by 14% and increase prostate cancer mortality by 2%. The model is open source and suitable for planning for effective prostate cancer screening into the future.

Activity, social and sexual behaviour in Red Junglefowl selected for divergent levels of fear of humans

The domesticated phenotype is a set of behavioural, morphological and physiological traits that is common for domesticated species. Previous research has found that selection for tameness only can give rise to correlated selection responses that resemble the domesticated phenotype. It has therefore been suggested that tameness may drive the domesticated phenotype as correlated traits. We selected Red Junglefowl for divergent levels of fear of human for eight generations and assessed possible correlated selection responses in other behaviours in semi-natural settings. Behavioural studies were carried out on birds from generations six to eight, and at different ages, in order to study possible effects on general activity, social behaviour and male courtship behaviour. We found that the differences between selection lines changed with age. Adult low fear birds were generally more active and high fear males showed a more intense courtship behaviour. Our study shows that several behaviours can be modified through correlated selection responses by selection on reduced fear of humans only, emphasising the putative role of tameness as a driver of domestication related phenotypes.

Relative survival in patients with dementia with Lewy bodies and Parkinson's disease dementia

INTRODUCTION

The understanding of survival in dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) is limited, as well as the impact of these diagnoses in an ageing co-morbid population.

METHODS

A retrospective study of 177 patients who received a DLB or PDD diagnosis between 1997-2014 at the Memory Clinic in Malmö, Sweden. Relative survival was evaluated by adjusting all-cause survival for expected survival, estimated from population life-tables, matched by sex, age and calendar year. Predictors of relative survival were investigated using multivariate regression modelling.

RESULTS

At follow-up, 143 (81%) patients were deceased with a median survival of 4.1 years (IQR 2.6-6.0). After 10-years follow-up, the standardized mortality ratio was 3.44 (95% CI 2.92-4.04). Relative survival was worse with younger age at diagnosis (excess hazard ratio [eHR] 0.91, 95% CI 0.88-0.94 per year of age), female sex (eHR 1.45, 95% CI 1.01-2.09) and lower mini-mental state examination (eHR 0.93, 95% CI 0.90-0.96). Subgroup analysis (n = 141) showed higher mortality in DLB patients who were positive for APOE ɛ4 (eHR 2.00, 95% CI 1.35-2.97).

CONCLUSION

The mortality is over three-times higher in patients diagnosed with dementia with Lewy bodies and Parkinson's disease dementia during a ten-year follow-up, compared to persons in the general population. Excess mortality is found primarily in younger patients, females and carriers of APOE ε4. Further research is needed regarding survival and possible interventions, including disease-modifying treatments, to improve care for this patient group.

Greater tau load and reduced cortical thickness in APOE ε4-negative Alzheimer's disease: a cohort study

BACKGROUND

Alzheimer's disease is characterized by aggregated β-amyloid and tau proteins, but the clinical presentations and patterns of brain atrophy vary substantially. A part of this heterogeneity may be linked to the risk allele APOE ε4. The spread of tau pathology is related to atrophy and cognitive decline, but little data exist on the effects of APOE ε4 on tau. The objective of this preliminary study was therefore to test if tau load and brain structure differ by APOE ε4 in Alzheimer's disease.

METHODS

Sixty-five β-amyloid-positive patients at the prodromal and dementia stages of Alzheimer's disease were enrolled, including APOE ε4-positive (n = 46) and APOE ε4-negative (n = 19) patients. 18F-AV-1451 positron emission tomography was used to measure tau and brain magnetic resonance imaging (MRI) was used to measure cortical thickness.

RESULTS

Compared with their APOE ε4-positive counterparts, APOE ε4-negative patients had greater tau load and reduced cortical thickness, with the most pronounced effects for both in the parietal cortex. Relative to the overall cortical tau load, APOE ε4-positive patients had greater tau load in the entorhinal cortex. APOE ε4-positive patients also had slightly greater cortical β-amyloid load. There was an interaction between APOE ε4 and 18F-AV-1451 on cortical thickness, with greater effects of 18F-AV-1451 on cortical thickness in APOE ε4-negative patients. APOE ε4 and 18F-AV-1451 were independent predictors of cognition, but showed distinct associations with different cognitive tests.

CONCLUSIONS

APOE genotype may be associated with differences in pathways in Alzheimer's disease, potentially through differential development and spread of tau, as well as through effects on cognitive outcomes involving non-tau-related mechanisms.

Feasibility of sun and magnetic compass mechanisms in avian long-distance migration

Birds use different compass mechanisms based on celestial (stars, sun, skylight polarization pattern) and geomagnetic cues for orientation. Yet, much remains to be understood how birds actually use these compass mechanisms on their long-distance migratory journeys. Here, we assess in more detail the consequences of using different sun and magnetic compass mechanisms for the resulting bird migration routes during both autumn and spring migration. First, we calculated predicted flight routes to determine which of the compasses mechanisms lead to realistic and feasible migration routes starting at different latitudes during autumn and spring migration. We then compared the adaptive values of the different compass mechanisms by calculating distance ratios in relation to the shortest possible trajectory for three populations of nocturnal passerine migrants: northern wheatear Oenanthe oenanthe, pied flycatcher Ficedula hypoleuca, and willow warbler Phylloscopus trochilus. Finally, we compared the predicted trajectories for different compass strategies with observed routes based on recent light-level geolocation tracking results for five individuals of northern wheatears migrating between Alaska and tropical Africa. We conclude that the feasibility of different compass routes varies greatly with latitude, migratory direction, migration season, and geographic location. Routes following a single compass course throughout the migratory journey are feasible for many bird populations, but the underlying compass mechanisms likely differ between populations. In many cases, however, the birds likely have to reorient once to a few times along the migration route and/or use map information to successfully reach their migratory destination.

Dual tracer tau PET imaging reveals different molecular targets for 11C-THK5351 and 11C-PBB3 in the Alzheimer brain

Purpose

Several tau PET tracers have been developed, but it remains unclear whether they bind to the same molecular target on the heterogeneous tau pathology. In this study we evaluated the binding of two chemically different tau-specific PET tracers (¹¹C-THK5351 and ¹¹C-PBB3) in a head-to-head, in vivo, multimodal design.

Methods

Nine patients with a diagnosis of mild cognitive impairment or probable Alzheimer’s disease and cerebrospinal fluid biomarker evidence supportive of the presence of Alzheimer’s disease brain pathology were recruited after thorough clinical assessment. All patients underwent imaging with the tau-specific PET tracers ¹¹C-THK5351 and ¹¹C-PBB3 on the same day, as well as imaging with the amyloid-beta-specific tracer ¹¹C-AZD2184, a T1-MRI sequence, and neuropsychological assessment.

Results

The load and regional distribution of binding differed between ¹¹C-THK5351 and ¹¹C-PBB3 with no statistically significant regional correlations observed between the tracers. The binding pattern of ¹¹C-PBB3, but not that of ¹¹C-THK5351, in the temporal lobe resembled that of ¹¹C-AZD2184, with strong correlations detected between ¹¹C-PBB3 and ¹¹C-AZD2184 in the temporal and occipital lobes. Global cognition correlated more closely with ¹¹C-THK5351 than with ¹¹C-PBB3 binding. Similarly, cerebrospinal fluid tau measures and entorhinal cortex thickness were more closely correlated with ¹¹C-THK5351 than with ¹¹C-PBB3 binding.

Conclusion

This research suggests different molecular targets for these tracers; while ¹¹C-PBB3 appeared to preferentially bind to tau deposits with a close spatial relationship to amyloid-beta, the binding pattern of ¹¹C-THK5351 fitted the expected distribution of tau pathology in Alzheimer’s disease better and was more closely related to downstream disease markers.

Electronic supplementary material

The online version of this article (10.1007/s00259-018-4012-5) contains supplementary material, which is available to authorized users.

Hemodynamic forces in the left and right ventricles of the human heart using 4D flow magnetic resonance imaging: Phantom validation, reproducibility, sensitivity to respiratory gating and free analysis software

Purpose

To investigate the accuracy, reproducibility and sensitivity to respiratory gating, field strength and ventricle segmentation of hemodynamic force quantification in the left and right ventricles of the heart (LV and RV) using 4D-flow magnetic resonance imaging (MRI), and to provide free hemodynamic force analysis software.

Materials and methods

A pulsatile flow phantom was imaged using 4D flow MRI and laser-based particle image velocimetry (PIV). Cardiac 4D flow MRI was performed in healthy volunteers at 1.5T (n = 23). Reproducibility was investigated using MR scanners from two different vendors on the same day (n = 8). Subsets of volunteers were also imaged without respiratory gating (n = 17), at 3T on the same day (n = 6), and 1–12 days later on the same scanner (n = 9, median 6 days). Agreement was measured using the intraclass correlation coefficient (ICC).

Results

Phantom validation showed good accuracy for both scanners (Scanner 1: bias -14±9%, y = 0.82x+0.08, R² = 0.96, Scanner 2: bias -12±8%, y = 0.99x-0.08, R² = 1.00). Force reproducibility was strong in the LV (0.09±0.07 vs 0.09±0.07 N, bias 0.00±0.04 N, ICC = 0.87) and RV (0.09±0.06 vs 0.09±0.05 N, bias 0.00±0.03, ICC = 0.83). Strong to very strong agreement was found for scans with and without respiratory gating (LV/RV: ICC = 0.94/0.95), scans on different days (ICC = 0.92/0.87), and 1.5T and 3T scans (ICC = 0.93/0.94).

Conclusion

Software for quantification of hemodynamic forces in 4D-flow MRI was developed, and results show high accuracy and strong to very strong reproducibility for both the LV and RV, supporting its use for research and clinical investigations. The software including source code is released freely for research.

Maternal suicide - Register based study of all suicides occurring after delivery in Sweden 1974-2009

Background

Recent research suggests that having a newborn child is associated with substantially reduced risk for maternal suicide. We studied postpartum suicides in a national cohort of mothers and the role of mental disorder, self-harm and delivery related factors.

Methods

We used a nested case-control design with data from Swedish registries. The cohort consisted of all women given birth in Sweden 1974–2009. Mothers who died by suicide during follow-up were considered cases (n = 1,786) and risk of suicide was estimated with proximity to delivery as the explanatory variable. In a second step, association between suicide during the first year following delivery (n = 145) and mental disorder, self-harm and delivery related variables risk factors were analyzed.

Results

The first postpartum year was associated with a lower risk of suicide, compared to later (RR 0.80, 95%CI 0.66–0.96), which was unaltered after adjustment for socio-economic status and history of self-harm (aRR 0.82, 95%CI 0.68–0.99). Compared to living mothers, suicide victims of the postpartum year more often had affective disorders (aRR 133.94, 95%CI 45.93–390.61), psychotic disorders (aRR 83.69, 95%CI 36.99–189.31) and history of self-harm (aRR 47.56, 95%CI 18.24–124.02). The aRR of stillbirth was 2.66 (95%CI 0.63–11.30).

Conclusions

We found only a weak negative association between childbirth during the preceding year and suicide, when using mothers as controls. A severe mental disorder after delivery and a history of self-harm was strongly associated with increased risk of suicide in the postpartum year and may inform the clinical assessment postpartum.

Discovery of the fourth mobile sulfonamide resistance gene

BACKGROUND

Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.

RESULTS

Up to 89% of identified open reading frames encode known resistance genes, or variations thereof (> 1000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.

CONCLUSIONS

Our findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.

Reduced kidney function is associated with BMD, bone loss and markers of mineral homeostasis in older women: a 10-year longitudinal study

Kidney function decreases with age; however, the long-term influence on bone density (BMD) in older women already at risk of osteoporosis is unknown. We followed kidney function and bone loss for 10 years. Declining kidney function was adversely associated with bone loss and mineral homeostasis in old women, though it attenuated with advanced aging.

INTRODUCTION

Existing studies do not fully address the relationship between kidney function and bone metabolism with advanced aging in Caucasian women. This study describes the association between kidney function, BMD, bone loss and bone metabolism in older women and provides a review of the available literature for context.

METHODS

We studied participants from the OPRA cohort with follow-up after 5 and 10 years. Using plasma cystatin C (cysC), estimated glomerular function rate (eGFR) was evaluated at age 75 (n = 981), 80 (n = 685) and 85 (n = 365). Women were stratified into "normal" function (CKD stages 1-2), "intermediate" (stage 3a) and "poor" (stages 3b-5), and outcome measures-BMD, bone loss and markers of mineral homeostasis-were compared.

RESULTS

Femoral neck (FN) BMD positively associated with kidney function at 75 years old ([Formula: see text] = 0.001, p = 0.028) and 80 years old ([Formula: see text] = 0.001, p = 0.001), although with small effect size. Prevalence of osteoporosis (FN T-score ≤ - 2.5) did not differ with kidney function. Measured at age 75, women with poor kidney function had higher annual percentage bone loss over 5 years compared to those with normal function (2.3%, 95% CI 1.8-2.8 versus 1.3%, 95% CI 1.1-1.5, p = 0.007), although not when measured from age 80 or 85. Additionally, markers of mineral homeostasis (PTH, phosphate, vitamin D, calcium), CRP and osteocalcin differed by kidney function.

CONCLUSIONS

In old women, kidney function is associated with BMD, bone loss and altered mineral homeostasis; probably, a relationship attenuated in the very elderly.

"I am Your Mother and Your Father!" In Vitro Derived Gametes and the Ethics of Solo Reproduction

In this paper, we will discuss the prospect of human reproduction achieved with gametes originating from only one person. According to statements by a minority of scientists working on the generation of gametes in vitro, it may become possible to create eggs from men's non-reproductive cells and sperm from women's. This would enable, at least in principle, the creation of an embryo from cells obtained from only one individual: 'solo reproduction'. We will consider what might motivate people to reproduce in this way, and the implications that solo reproduction might have for ethics and policy. We suggest that such an innovation is unlikely to revolutionise reproduction and parenting. Indeed, in some respects it is less revolutionary than in vitro fertilisation as a whole. Furthermore, we show that solo reproduction with in vitro created gametes is not necessarily any more ethically problematic than gamete donation-and probably less so. Where appropriate, we draw parallels with the debate surrounding reproductive cloning. We note that solo reproduction may serve to perpetuate reductive geneticised accounts of reproduction, and that this may indeed be ethically questionable. However, in this it is not unique among other technologies of assisted reproduction, many of which focus on genetic transmission. It is for this reason that a ban on solo reproduction might be inconsistent with continuing to permit other kinds of reproduction that also bear the potential to strengthen attachment to a geneticised account of reproduction. Our claim is that there are at least as good reasons to pursue research towards enabling solo reproduction, and eventually to introduce solo reproduction as an option for fertility treatment, as there are to do so for other infertility related purposes.

PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants

Altogether 95 children with primary bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Two children with multiple peripheral and spinal fractures and low BMD had novel disease-causing PLS3 variants. Children with milder phenotypes had no pathogenic variants. PLS3 screening is indicated in childhood-onset primary osteoporosis.

INTRODUCTION

The study aimed to determine the role of pathogenic PLS3 variants in children's bone fragility and to elucidate the associated phenotypic features.

METHODS

Two cohorts of children with bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Cohort I comprised 31 patients with childhood-onset primary osteoporosis of unknown etiology. Cohort II comprised 64 children who had sustained multiple fractures but were otherwise healthy. Clinical and radiological data were reviewed. Peripheral blood DNA was Sanger sequenced for coding exons and flanking intronic regions of PLS3.

RESULTS

In two patients of cohort I, where other common genetic causes had been excluded, we identified two novel disease-causing PLS3 variants. Patient 1 was a male with bilateral femoral fractures at 10 years, low BMD (Z-score -4.1; 18 years), and multiple vertebral compression fractures. He had a novel nonsense variant in PLS3. Patient 2 was a girl with multiple long bone and vertebral fractures and low BMD (Z-score -6.6 at 6 years). She had a de novo missense variant in PLS3; whole exome sequencing and array-CGH identified no other genetic causes. Iliac crest bone biopsies confirmed low-turnover osteoporosis in both patients. In cohort II, no pathogenic PLS3 variants were identified in any of the subjects.

CONCLUSIONS

Two novel disease-causing variants in PLS3 were identified in a boy and a girl with multiple peripheral and spinal fractures and very low BMD while no pathogenic variants were identified in children with less severe skeletal fragility. PLS3 screening is warranted in male and female patients with childhood-onset primary osteoporosis.

Asporin-deficient mice have tougher skin and altered skin glycosaminoglycan content and structure

The main structural component of connective tissues is fibrillar, cross-linked collagen whose fibrillogenesis can be modulated by Small Leucine-Rich Proteins/Proteoglycans (SLRPs). Not all SLRPs’ effects on collagen and extracellular matrix in vivo have been elucidated; one of the less investigated SLRPs is asporin. Here we describe the successful generation of an Aspn^-/- mouse model and the investigation of the Aspn^-/- skin phenotype. Functionally, Aspn^-/- mice had an increased skin mechanical toughness, although there were no structural changes present on histology or immunohistochemistry. Electron microscopy analyses showed 7% thinner collagen fibrils in Aspn^-/- mice (not statistically significant). Several matrix genes were upregulated, including collagens (Col1a1, Col1a2, Col3a1), matrix metalloproteinases (Mmp2, Mmp3) and lysyl oxidases (Lox, Loxl2), while lysyl hydroxylase (Plod2) was downregulated. Intriguingly no differences were observed in collagen protein content or in collagen cross-linking-related lysine oxidation or hydroxylation. The glycosaminoglycan content and structure in Aspn^-/- skin was profoundly altered: chondroitin/dermatan sulfate was more than doubled and had an altered composition, while heparan sulfate was halved and had a decreased sulfation. Also, decorin and biglycan were doubled in Aspn^-/- skin. Overall, asporin deficiency changes skin glycosaminoglycan composition, and decorin and biglycan content, which may explain the changes in skin mechanical properties.

Microwave technology for detecting traumatic intracranial bleedings: tests on phantom of subdural hematoma and numerical simulations

Traumatic brain injury is the leading cause of death and severe disability for young people and a major public health problem for elderly. Many patients with intracranial bleeding are treated too late, because they initially show no symptoms of severe injury and are not transported to a trauma center. There is a need for a method to detect intracranial bleedings in the prehospital setting. In this study, we investigate whether broadband microwave technology (MWT) in conjunction with a diagnostic algorithm can detect subdural hematoma (SDH). A human cranium phantom and numerical simulations of SDH are used. Four phantoms with SDH 0, 40, 70 and 110 mL are measured with a MWT instrument. The simulated dataset consists of 1500 observations. Classification accuracy is assessed using fivefold cross-validation, and a validation dataset never used for training. The total accuracy is 100 and 82-96 % for phantom measurements and simulated data, respectively. Sensitivity and specificity for bleeding detection were 100 and 96 %, respectively, for the simulated data. SDH of different sizes is differentiated. The classifier requires training dataset size in order of 150 observations per class to achieve high accuracy. We conclude that the results indicate that MWT can detect and estimate the size of SDH. This is promising for developing MWT to be used for prehospital diagnosis of intracranial bleedings.

The importance of nonlinear tissue modelling in finite element simulations of infant head impacts

Despite recent efforts on the development of finite element (FE) head models of infants, a model capable of capturing head responses under various impact scenarios has not been reported. This is hypothesized partially attributed to the use of simplified linear elastic models for soft tissues of suture, scalp and dura. Orthotropic elastic constants are yet to be determined to incorporate the direction-specific material properties of infant cranial bone due to grain fibres radiating from the ossification centres. We report here on our efforts in advancing the above-mentioned aspects in material modelling in infant head and further incorporate them into subject-specific FE head models of a newborn, 5- and 9-month-old infant. Each model is subjected to five impact tests (forehead, occiput, vertex, right and left parietal impacts) and two compression tests. The predicted global head impact responses of the acceleration-time impact curves and the force-deflection compression curves for different age groups agree well with the experimental data reported in the literature. In particular, the newly developed Ogden hyperelastic model for suture, together with the nonlinear modelling of scalp and dura mater, enables the models to achieve more realistic impact performance compared with linear elastic models. The proposed approach for obtaining age-dependent skull bone orthotropic material constants counts both an increase in stiffness and decrease in anisotropy in the skull bone-two essential biological growth parameters during early infancy. The profound deformation of infant head causes a large stretch at the interfaces between the skull bones and the suture, suggesting that infant skull fractures are likely to initiate from the interfaces; the impact angle has a profound influence on global head impact responses and the skull injury metrics for certain impact locations, especially true for a parietal impact.

Estimation of Nonlinear Adsorption Isotherms in Gradient Elution RP-LC of Peptides in the Presence of an Adsorbing Additive

ABSTRACT

In electrostatic repulsive interaction chromatography, using a charged surface hybrid sorbent carrying positive charges can improve the peak shape of peptides in reversed-phase liquid chromatography (RP-LC), especially in overloaded conditions, compared with standard C18 sorbents. However, the positive surface charges can interact with anionic additives commonly used in peptide separations, e.g., trifluoroacetic acid (TFA), complicating adsorption isotherm estimation. We investigated how the competition for available adsorption sites between TFA and two peptides influenced the adsorption isotherm in gradient elution. A model accounting for the competition with TFA was compared with a model neglecting TFA adsorption. We found that the two models predicted elution profiles with the same accuracy. We also found that the adsorption isotherms were extremely similar in shape, leading to the conclusion that neglecting the competition with TFA is a valid approximation enabling faster and more robust adsorption isotherm estimation for the studied type of sorbent.

GRAPHICAL ABSTRACT

Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters

BACKGROUND

Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere.

RESULTS

In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria.

CONCLUSIONS

Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.

Human ROBO1 regulates white matter structure in corpus callosum

The axon guidance receptor, Robo1, controls the pathfinding of callosal axons in mice. To determine whether the orthologous ROBO1 gene is involved in callosal development also in humans, we studied polymorphisms in the ROBO1 gene and variation in the white matter structure in the corpus callosum using both structural magnetic resonance imaging and diffusion tensor magnetic resonance imaging. We found that five polymorphisms in the regulatory region of ROBO1 were associated with white matter density in the posterior part of the corpus callosum pathways. One of the polymorphisms, rs7631357, was also significantly associated with the probability of connections to the parietal cortical regions. Our results demonstrate that human ROBO1 may be involved in the regulation of the structure and connectivity of posterior part of corpus callosum.

Asymptotic Robustness Study of the Polychoric Correlation Estimation

Asymptotic robustness against misspecification of the underlying distribution for the polychoric correlation estimation is studied. The asymptotic normality of the pseudo-maximum likelihood estimator is derived using the two-step estimation procedure. The t distribution assumption and the skew-normal distribution assumption are used as alternatives to the normal distribution assumption in a numerical study. The numerical results show that the underlying normal distribution can be substantially biased, even though skewness and kurtosis are not large. The skew-normal assumption generally produces a lower bias than the normal assumption. Thus, it is worth using a non-normal distributional assumption if the normal assumption is dubious.

Setting development goals using stochastic dynamical system models

The Millennium Development Goals (MDG) programme was an ambitious attempt to encourage a globalised solution to important but often-overlooked development problems. The programme led to wide-ranging development but it has also been criticised for unrealistic and arbitrary targets. In this paper, we show how country-specific development targets can be set using stochastic, dynamical system models built from historical data. In particular, we show that the MDG target of two-thirds reduction of child mortality from 1990 levels was infeasible for most countries, especially in sub-Saharan Africa. At the same time, the MDG targets were not ambitious enough for fast-developing countries such as Brazil and China. We suggest that model-based setting of country-specific targets is essential for the success of global development programmes such as the Sustainable Development Goals (SDG). This approach should provide clear, quantifiable targets for policymakers.

Matrix Riemann-Hilbert problems with jumps across Carleson contours

We develop a theory of n × n -matrix Riemann-Hilbert problems for a class of jump contours and jump matrices of low regularity. Our basic assumption is that the contour Γ is a finite union of simple closed Carleson curves in the Riemann sphere. In particular, unbounded contours with cusps, corners, and nontransversal intersections are allowed. We introduce a notion of L p -Riemann-Hilbert problem and establish basic uniqueness results and Fredholm properties. We also investigate the implications of Fredholmness for the unique solvability and prove a theorem on contour deformation.

Prediction of femoral strength using 3D finite element models reconstructed from DXA images: validation against experiments

Computed tomography (CT)-based finite element (FE) models may improve the current osteoporosis diagnostics and prediction of fracture risk by providing an estimate for femoral strength. However, the need for a CT scan, as opposed to the conventional use of dual-energy X-ray absorptiometry (DXA) for osteoporosis diagnostics, is considered a major obstacle. The 3D shape and bone mineral density (BMD) distribution of a femur can be reconstructed using a statistical shape and appearance model (SSAM) and the DXA image of the femur. Then, the reconstructed shape and BMD could be used to build FE models to predict bone strength. Since high accuracy is needed in all steps of the analysis, this study aimed at evaluating the ability of a 3D FE model built from one 2D DXA image to predict the strains and fracture load of human femora. Three cadaver femora were retrieved, for which experimental measurements from ex vivo mechanical tests were available. FE models were built using the SSAM-based reconstructions: using only the SSAM-reconstructed shape, only the SSAM-reconstructed BMD distribution, and the full SSAM-based reconstruction (including both shape and BMD distribution). When compared with experimental data, the SSAM-based models predicted accurately principal strains (coefficient of determination >0.83, normalized root-mean-square error <16%) and femoral strength (standard error of the estimate 1215 N). These results were only slightly inferior to those obtained with CT-based FE models, but with the considerable advantage of the models being built from DXA images. In summary, the results support the feasibility of SSAM-based models as a practical tool to introduce FE-based bone strength estimation in the current fracture risk diagnostics.