Genome-scale metabolic network models for industrial microorganisms metabolic engineering: Current advances and future prospects

The construction of high-performance microbial cell factories (MCFs) is the centerpiece of biomanufacturing. However, the complex metabolic regulatory network of microorganisms poses great challenges for the efficient design and construction of MCFs. The genome-scale metabolic network models (GSMs) can systematically simulate the metabolic regulation process of microorganisms in silico, providing effective guidance for the rapid design and construction of MCFs. In this review, we summarized the development status of 16 important industrial microbial GSMs, and further outline the technologies or methods that continuously promote high-quality GSMs construction from five aspects: I) Databases and modeling tools facilitate GSMs reconstruction; II) evolving gap-filling technologies; III) constraint-based model reconstruction; IV) advances in algorithms; and V) developed visualization tools. In addition, we also summarized the applications of GSMs in guiding metabolic engineering from four aspects: I) exploring and explaining metabolic features; II) predicting the effects of genetic perturbations on metabolism; III) predicting the optimal phenotype; IV) guiding cell factories construction in practical experiment. Finally, we discussed the development of GSMs, aiming to provide a reference for efficiently reconstructing GSMs and guiding metabolic engineering.

Clustering of predicted loss-of-function variants in genes linked with monogenic disease can explain incomplete penetrance

BACKGROUND

Genetic variants that severely alter protein products (e.g. nonsense, frameshift) are often associated with disease. For some genes, these predicted loss-of-function variants (pLoFs) are observed throughout the gene, whilst in others, they occur only at specific locations. We hypothesised that, for genes linked with monogenic diseases that display incomplete penetrance, pLoF variants present in apparently unaffected individuals may be limited to regions where pLoFs are tolerated. To test this, we investigated whether pLoF location could explain instances of incomplete penetrance of variants expected to be pathogenic for Mendelian conditions.

METHODS

We used exome sequence data in 454,773 individuals in the UK Biobank (UKB) to investigate the locations of pLoFs in a population cohort. We counted numbers of unique pLoF, missense, and synonymous variants in UKB in each quintile of the coding sequence (CDS) of all protein-coding genes and clustered the variants using Gaussian mixture models. We limited the analyses to genes with ≥ 5 variants of each type (16,473 genes). We compared the locations of pLoFs in UKB with all theoretically possible pLoFs in a transcript, and pathogenic pLoFs from ClinVar, and performed simulations to estimate the false-positive rate of non-uniformly distributed variants.

RESULTS

For most genes, all variant classes fell into clusters representing broadly uniform variant distributions, but genes in which haploinsufficiency causes developmental disorders were less likely to have uniform pLoF distribution than other genes (P < 2.2 × 10-6). We identified a number of genes, including ARID1B and GATA6, where pLoF variants in the first quarter of the CDS were rescued by the presence of an alternative translation start site and should not be reported as pathogenic. For other genes, such as ODC1, pLoFs were located approximately uniformly across the gene, but pathogenic pLoFs were clustered only at the end, consistent with a gain-of-function disease mechanism.

CONCLUSIONS

Our results suggest the potential benefits of localised constraint metrics and that the location of pLoF variants should be considered when interpreting variants.

Constraints-related microscopic fatigue crack propagation behaviour of polycrystalline alloys

Based on the microscopic polycrystalline fatigue crack propagation (MPFCP) model, the MPFCP behaviours of GH4169 alloy under different micro-notch depths and lengths (constraints) were studied from aspects of MPFCP path, MPFCP rate and stress distribution. The influences of the initial crack angle on MPFCP behaviour were further explored. It was observed that the grain boundary, the grain size and the stress state were different during crack propagation under different constraints, resulting in different MPFCP paths. The MPFCP path was straighter under high constraints, and the MPFCP rate was related to the micro-notch size and the loading direction. The crack tip needed more stress accumulation at low constraints than under high constraints to ensure smooth MPFCP behaviour. The influence of the initial crack angle on the MPFCP path was mainly reflected in the grain interior where the initial crack was located. The initial crack angle had a greater influence on the MPFCP rate than on the MPFCP path.

The organization of ethnocultural attachments among second- generation Germans

Recent research suggests that two ethnocultural "identities"-such as ethnic identity or national identity-can be compatible (positively correlated) or in conflict (negatively correlated) within and across immigrant-origin groups. In the present article, I advance a more cognitively oriented framework for using correlational patterns to map how immigrant-origin people organize their attachments to a variety of ethnocultural categories. In explaining the value of this framework, I embark on a multistage empirical illustration. First, I perform a correlational class analysis (CCA) using a sample of second-generation Germans and a vector of 13 identity-related indicators. Second, I use a series of linear regressions and a descriptive visualization to clarify the results of my CCA. Third, I fit two multinomial logistic regressions that demonstrate how social attributes-and specifically, religion and ethnicity-impose constraints on the latent schemes that second-generation Germans follow to organize their ethnocultural "identities."

A mathematical formula of plasticity: Measuring susceptibility to change in mental health and data science

Plasticity is increasingly recognized as a critical concept in psychiatry and mental health because it allows the reorganization of neural circuits and behavior during the transition from psychopathology to wellbeing. Differences in individual plasticity may explain why therapies, such as psychotherapeutic and environmental interventions, are highly effective in some but not in all patients. Here I propose a mathematical formula to assess plasticity - i.e., the susceptibility to change - to identify, at baseline, which individuals or populations are more likely to modify their behavioral outcome according to therapies or contextual factors. The formula is grounded in the network theory of plasticity so that, when representing a system (e.g., a patient's psychopathology) as a weighed network where the nodes are the system features (e.g., symptoms) and the edges are the connections (i.e., correlations) among them, the network connectivity strength is an inverse measure of the plasticity of the system: the weaker the connectivity, the higher the plasticity and the greater the susceptibility to change. The formula is predicted to be generalizable, measuring plasticity at multiple scales, from the single cell to the whole brain, and can be applied to a wide range of research fields, including neuroscience, psychiatry, ecology, sociology, physics, market and finance.

Effects of rabbit production on income and livelihood of rural households in Nigeria

Aims

More effort and actions are needed to combat the rising levels of food insecurity and poverty in developing countries, particularly among rural households. Rural households can significantly contribute to reducing poverty, enhancing their nutritional condition, and enhancing their standard of living by engaging in rabbit production but there are few empirical studies on the contribution of rabbit production to households' livelihood and income. Therefore, this study examines how producing rabbits affects rural farmers' income and household livelihood in Nigeria.

Methods and results

Multiple regression and descriptive statistics were used to analyze the data gathered from 240 rabbit farms. The findings demonstrated that rabbit farming is a male-dominated enterprise (male 77.5%). According to the regression analysis, the income of rural households was positively and significantly impacted by the income from rabbits. Farmers' ages, interactions with extension agents, credit they accessed, and assets were further determinants of their income. Additionally, rabbit production improved the level of living of rural households. Access to forage, the prevalence of diseases, scarcity of veterinary, and the high cost of medication, were the severe constraints faced in rabbit production.

Conclusions

It may be concluded that rabbit production had a significant contribution to the economic situation, way of life, and well-being of rural households. Although there were some constraints with the operation. Females are to be encouraged in rabbit production as livelihood diversification. Also, it is crucial that banks, governments, and non-governmental organizations offer farmers easily accessible and reasonable loan facilities as this will boost their revenue. Training on forage production and storage is also recommended.

Significance and the impact of the study

Participation will be improved by having an understanding of how rabbit farming affects the income and way of life of rural dwellers. As a result, the findings of this study would enable policymakers to intervene in enhancing its production thereby encouraging more farmers to be involved in the production and also, enhancing the well-being of rural households.

Dialysis Patients' Social Networks and Living Donation Offers

Rationale & Objective

Most living kidney donors are members of a hemodialysis patient's social network. Network members are divided into core members, those strongly connected to the patient and other members; and peripheral members, those weakly connected to the patient and other members. We identify how many hemodialysis patients' network members offered to become kidney donors, whether these offers were from core or peripheral network members, and whose offers the patients accepted.

Study Design

A cross-sectional interviewer-administered hemodialysis patient social network survey.

Setting & Participants

Prevalent hemodialysis patients in 2 facilities.

Predictors

Network size and constraint, a donation from a peripheral network member.

Outcomes

Number of living donor offers, accepting an offer.

Analytical Approach

We performed egocentric network analyses for all participants. Poisson regression models evaluated associations between network measures and number of offers. Logistic regression models determined the associations between network factors and accepting a donation offer.

Results

The mean age of the 106 participants was 60 years. Forty-five percent were female, and 75% self-identified as Black. Fifty-two percent of participants received at least one living donor offer (range 1-6); 42% of the offers were from peripheral members. Participants with larger networks received more offers (incident rate ratio [IRR], 1.26; 95% CI, 1.12-1.42; P = 0.001), including networks with more peripheral members (constraint, IRR, 0.97; 95% CI, 0.96-0.98; P < 0.001). Participants who received a peripheral member offer had 3.6 times greater odds of accepting an offer (OR, 3.56; 95% CI, 1.15-10.8; P = 0.02) than those who did not receive a peripheral member offer.

Limitations

A small sample of only hemodialysis patients.

Conclusions

Most participants received at least one living donor offer, often from peripheral network members. Future living donor interventions should focus on both core and peripheral network members.

Constraint degree in revision total knee replacement: a registry study on 1432 patients

PURPOSE

Total knee replacement (TKR) failure represents a hard challenge for knee surgeons. TKR failure can be managed in revision with different constraint, related with soft and bone knee damages. The choice of the right constraint for every failure cause represents a not summarized entity. The purpose of this study is identifying distribution of different constraints in revision TKR (rTKR) for failure cause and the overall survival.

METHODS

A registry study based on the Emilia Romagna Register of the Orthopaedic Prosthetic Implants (called RIPO) was performed with a selection of 1432 implants, in the period between 2000 and 2019. Selection implants including primary surgery constraint, failure cause and constraint revision for every patient, and divided for constraint degrees used during procedures (Cruciate Retaining-CR, Posterior Stabilized-PS, Condylar Constrained Knee-CCK, Hinged).

RESULTS

The most common cause of primary TKR failure was aseptic loosening (51,45%), followed by septic loosening (29,12%). Each type of failure was managed with different constraint, the most used was CCK in the most of failure causes, such as to manage aseptic and septic loosening in CR and PS failure. Overall survival of TKA revisions has been calculated at 5 and 10 years for each constraint, with a range of 75.1-90.0% at 5 years and 75.1-87.5% at 10 years.

CONCLUSION

Constraint degree in rTKR is typically higher than primary, CCK is the most used constraint in revision surgery with an overall survival of 87.5% at 10 years.

The rise and fall of onion production; its multiple constraints on pre-harvest and post-harvest management issues along the supply chain in northwest Ethiopia

Food and nutrition security is not only addressed by increasing production alone, it should also ensure by reducing food loss. Onion has a great contribution to both economic and health issues, however, its production and productivity in the country is low. Thus, the study was initiated to identify multiple constraints on onion production and postharvest handling practices and to determine the extent of postharvest loss along the supply chain in northwestern Ethiopia. The survey was conducted on production, marketing, and consumption at farm, wholesale, retailer, and consumers level. The multistage sampling procedure was employed. The present results revealed that sex, age, educational level, production experience, land covered by onion, and household size has a significant influence on onion production. Sex, age, education level, active household size, selling experience, amount purchased, and storage duration have a significant association with onion production and postharvest loss. Major onion production and post-harvest loss constraints were high perishability, nature of the crop, market, linkage problem and low market price, lack of awareness of using post-harvest technologies, absence of better storable varieties, shortage of fertilizer access, disease and insect pests. The whole purchased produce never reached the consumer's hands. The total postharvest loss of onion at the farmer, wholesale, retail, and consumer level was found to be 29.775%, of which the higher proportion of losses (35.5%) was observed at the farmer's level. Based on the findings of the present study, onion producers were challenged by timely and adequate supplies and unfair, high cost of major production inputs, and high post-harvest loss. Therefore, producers and handlers in each supply chain need to be trained on affordable and applicable postharvest technologies. In addition, continuous capacity-building training, improving infrastructures, and input access along the supply chain should be designed and implemented to improve better crop management and postharvest handling practices. Moreover, marketing cooperatives working on onion postharvest handling and marketing systems should be functional to absorb surplus production and ensure continuous supply to the market. Thus, meaningful interventions in the development and implementation of policy on sustainable production, handling practices, and supply of onion should be designed.

A storytree-based model for inter-document causal relation extraction from news articles

With more and more news articles appearing on the Internet, discovering causal relations between news articles is very important for people to understand the development of news. Extracting the causal relations between news articles is an inter-document relation extraction task. Existing works on relation extraction cannot solve it well because of the following two reasons: (1) most relation extraction models are intra-document models, which focus on relation extraction between entities. However, news articles are many times longer and more complex than entities, which makes the inter-document relation extraction task harder than intra-document. (2) Existing inter-document relation extraction models rely on similarity information between news articles, which could limit the performance of extraction methods. In this paper, we propose an inter-document model based on storytree information to extract causal relations between news articles. We adopt storytree information to integer linear programming (ILP) and design the storytree constraints for the ILP objective function. Experimental results show that all the constraints are effective and the proposed method outperforms widely used machine learning models and a state-of-the-art deep learning model, with F1 improved by more than 5% on three different datasets. Further analysis shows that five constraints in our model improve the results to varying degrees and the effects on the three datasets are different. The experiment about link features also suggests the positive influence of link information.

Constraint in complex primary total knee arthroplasty: rotating hinge versus condylar constrained implants

INTRODUCTION

Condylar constrained knee arthroplasties (CCKAs) and rotating hinge knee arthroplasties (RHKAs) achieved good outcomes in complex primary total knee arthroplasties (TKAs); however, long-term comparative studies are few. Using an arthroplasty registry, we sought to assess and compare in CCKAs and RHKAs: (1) the intra-operative rates of complications, (2) the survival rates, (3) the reasons for revision, and (4) the adjusted hazard ratios for failure.

MATERIALS AND METHODS

1432 constrained implants in primary TKAs performed for non-oncological indications were included: 703 RHKAs, 729 CCKAs. The two groups were comparable regarding age and gender. Kaplan-Meier curves were used to compare survival rates, multivariate analyses to assess the hazard ratios for failures.

RESULTS

The mean follow-up was 4.1 years (range 0-16.3) for CCKAs and 6.8 years (0-18.1) for RHKAs. The intra/peri-operative complications were similar in both the cohorts, with similar rates of femoral and tibial fractures. 10-year implant survival rates were similar in both the cohorts (91.9%, CI 95% 89.2-93.9% in RHKAs; 93.4%, CI 95% 90.3-95.6% in CCKAs). Periprosthetic infection was the most common reason for revision in the two cohorts, followed by aseptic loosening. Breakage occurred in 3 RHKAs (0.4%). CCKAs and RHKAs had a similar distribution of revision causes. Males aged less than 60 had significantly more failures, regardless the constraint degree. Unstemmed CCKAs significantly failed more than RHKAs and stemmed CCKAs.

CONCLUSIONS

Both modern CCKAs and RHKAs are viable long-term solutions in complex primary TKAs. More failures should be expected in males aged less than 60.

LEVEL OF EVIDENCE

IV, Therapeutic study.

The organization of political belief networks: A cross-country analysis

Studies on mass opinion conceptualize political ideology as an interrelated network of attitudes, beliefs and values. Using the joint dataset of European Values Study and World Values Survey collected between 2017 and 2020, I ask whether the organization of political ideology depends on the structure of political field. Consistent with the theories of social constraint, I find that in countries with high institutionalization of political parties, the organization of political opinions is more likely to be dense and consolidated. These patterns are robust to a variety of predictors between countries and the results are not sensitive to sampling variability or item selection.

Making People Autonomous: A Sociological Analysis of the Uses of Contracts and Projects in the Psychiatric Care Institutions

This article aims at describing the tensions arising from working on and with someone in psychiatry, in order to make this person more "autonomous". First, through the example of the recovery, it acknowledges, the normative horizon of what is considered today as "good care": a negotiation between partners, aiming at increasing the possibilities for everyone to follow their own lifestyle. It then seeks to describe how this definition of good care is endorsed and applied in two institutions (in Belgium and in France) hosting people with severe mental health issues where the care teams are using three words ("contract", "project" and "autonomy"). The article analyses the difficulties encountered while putting into practice these demanding ideals and shows how and to what end the care teams take action in defining the "good" projects and, in a more general way, what patients can or should expect from themselves and from their future.

Organization needs organization: Understanding integrated control in living organisms

Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and compare these two accounts of organization and argue that understanding biological organisms as cohesively integrated systems benefits from insights from both. To bring together the two accounts, we focus on the notions of control and regulation as bridge concepts. We start from a characterization of biological mechanisms in terms of constraints and focus on a specific type of mechanism, control mechanisms, that operate on other mechanisms on the basis of measurements of variables in the system and its environment. Control mechanisms are characterized by their own set of constraints that enable them to sense conditions, convey signals, and effect changes on constraints in the controlled mechanism. They thereby allow living organisms to adapt to internal and external variations and to coordinate their parts in such a manner as to maintain viability. Because living organisms contain a vast number of control mechanisms, a central challenge is to understand how they are themselves organized. With the support of examples from both unicellular and multicellular systems we argue that control mechanisms are organized heterarchically, and we discuss how this type of control architecture can, without invoking top-down and centralized forms of organizations, succeed in coordinating internal activities of organisms.

Reconciling the bottom-up methodology and ground measurement constraints to improve the city-scale NMVOCs emission inventory: A case study of Nanjing, China

Reliable emission estimate of non-methane volatile organic compounds (NMVOCs) is important for understanding the atmospheric chemistry and formulating control policy of ozone (O₃). In this study, a speciated emission inventory of anthropogenic NMVOCs was developed with the refined "bottom-up" methodology and best available information of individual sources for Nanjing in 2017. The total NMVOCs emissions were calculated at 163.2 Gg. It was broken down into the emissions of over 500 individual species and aromatics took the largest fraction (33.3% of the total emissions). Meanwhile, 105 compounds were measured at 5 sites representing different functional zones of Nanjing for one year. The annual mean concentration of totally 105 species varied from 48.5 ppbv to 63.7 ppbv, and alkanes was the most abundant group with its mass fractions ranging 37.2-40.1% at different sites. Constrained by the emission ratios of individual species versus carbon monoxide (CO) based on ground measurement, the total emissions of 105 species (NMVOCs-105) was estimated at 195.6 Gg, 81.1% larger than the bottom-up estimate of NMVOCs-105 (108.0 Gg). The constrained emissions indicated an overestimation of aromatics and underestimation of OVOCs and halocarbons in the bottom-up emission inventory because of the uncertainties in source profiles. O₃ simulation with Community Multi-scale Air Quality (CMAQ) model was conducted for January, April, July and October in 2017 to evaluate the bottom-up and constrained emission estimates. The mean normal bias (MNB) and mean normal error (MNE) values were generally within the criteria (MNB ≤ ±15% and MNE ≤ 30%) for both inventories. The model performance was improved when the constrained estimates were applied, indicating the benefit of ground observation constraints on NMVOCs emission estimation and O₃ simulation. Based on the O₃ formation potential (OFP), 12 key NMVOCs species mainly from surface coating, on-road vehicles and oil exploitation and refinery were identified as the priority compounds for O₃ reduction.

Early origins of divergent patterns of morphological evolution on the mammal and reptile stem-lineages

The origin of amniotes 320 million years ago signaled independence from water in vertebrates and was closely followed by divergences within the mammal and reptile stem lineages (Synapsida and Reptilia). Early members of both groups had highly similar morphologies, being superficially “lizard-like” forms with many plesiomorphies. However, the extent to which they might have exhibited divergent patterns of evolutionary change, with the potential to explain the large biological differences between their living members, is unresolved. We use a new, comprehensive phylogenetic dataset to quantify variation in rates and constraints of morphological evolution among Carboniferous–early Permian amniotes. We find evidence for an early burst of evolutionary rates, resulting in the early origins of morphologically distinctive subgroups that mostly persisted through the Cisuralian. Rates declined substantially through time, especially in reptiles. Early reptile evolution was also more constrained compared with early synapsids, exploring a more limited character state space. Postcranial innovation in particular was important in early synapsids, potentially related to their early origins of large body size. In contrast, early reptiles predominantly varied the temporal region, suggesting disparity in skull and jaw kinematics, and foreshadowing the variability of cranial biomechanics seen in reptiles today. Our results demonstrate that synapsids and reptiles underwent an early divergence of macroevolutionary patterns. This laid the foundation for subsequent evolutionary events and may be critical in understanding the substantial differences between mammals and reptiles today. Potential explanations include an early divergence of developmental processes or of ecological factors, warranting cross-disciplinary investigation. [Amniote; body size; constraint; phylogeny; rate.]

Double punch to the better than nothing: physical activity participation of adolescents with autism spectrum disorder

Participation in physical activity (PA) occurs differently in each individual. Investigating how it comes about in adolescents with autism spectrum disorder (ASD) is seen as an area that does not receive enough attention. In this paper, which was designed to get more information and contribute to the field, the participation of adolescents with ASD in PA was examined in line with the socio-ecological model through the opinions of 17 Turkish parents. Semi-structured interviews well-used to understand the perspective of parents', and as a main themes constraints and facilitating factors affecting participation of adolescents with ASD in PA were determined. When investigated in terms of intrapersonal factors, which are the first stage of the model, are examined, it is seen that ASD related problems as a constraint and experiences as a facilitator were the foremost themes. Interpersonal constraints were prejudice and family attitude while facilitators were family attitude and attitude of close surroundings. In environmental factors, the main constraints were adapted physical activity (APA) opportunities, while facilitators were neighborhood and facilities. While negative PA approaches of organizations was an institutional constraint, positive PA approach of organizations was a facilitator. In the final stages of the model, in terms of public policy, the constraint was not meeting expectations of current policies and the facilitator was improvements in policies. Consequently, it was understood that adolescents with ASD still participate in PA in some way even though they encounter many constraints when participating in physical activities, the constraints outweigh the facilitating factors.

Adaptation of a marine diatom to ocean acidification and warming reveals constraints and trade-offs

Ocean acidification and warming are recognized as two major anthropogenic perturbations of the modern ocean. However, little is known about the adaptive response of phytoplankton to them. Here we examine the adaptation of a marine diatom Thalassiosira weissflogii to ocean acidification in combination with ocean warming. Our results show that ocean warming have a greater effect than acidification on the growth of T. weissflogii over the long-term selection experiment (~380 generations), as well as many temperature response traits (e.g., optimum temperatures for photosynthesis, maximal net photosynthetic oxygen evolution rates, activation energy) in thermal reaction norm. These results suggest that ocean warming is the main driver for the evolution of the marine diatom T. weissflogii, rather than oceanacidification. However, the evolution resulting from warming can be constrained by ocean acidification, where ocean warming did not impose any effects at high CO₂ level. Furthermore, adaptations to ocean warming alone or to the combination of ocean acidification and warming come with trade-offs by inhibiting photochemical performances. The constrains and trade-offs associated with the adaptation to ocean acidification and warming demonstrated in this study, should be considered for parameterizing evolutionary responses in eco-evolutionary models of phytoplankton dynamics in a future ocean.

An agent-based model clarifies the importance of functional and developmental integration in shaping brain evolution

Background

Vertebrate brain structure is characterised not only by relative consistency in scaling between components, but also by many examples of divergence from these general trends.. Alternative hypotheses explain these patterns by emphasising either ‘external’ processes, such as coordinated or divergent selection, or ‘internal’ processes, like developmental coupling among brain regions. Although these hypotheses are not mutually exclusive, there is little agreement over their relative importance across time or how that importance may vary across evolutionary contexts.

Results

We introduce an agent-based model to simulate brain evolution in a ‘bare-bones’ system and examine dependencies between variables shaping brain evolution. We show that ‘concerted’ patterns of brain evolution do not, in themselves, provide evidence for developmental coupling, despite these terms often being treated as synonymous in the literature. Instead, concerted evolution can reflect either functional or developmental integration. Our model further allows us to clarify conditions under which such developmental coupling, or uncoupling, is potentially adaptive, revealing support for the maintenance of both mechanisms in neural evolution. Critically, we illustrate how the probability of deviation from concerted evolution depends on the cost/benefit ratio of neural tissue, which increases when overall brain size is itself under constraint.

Conclusions

We conclude that both developmentally coupled and uncoupled brain architectures can provide adaptive mechanisms, depending on the distribution of selection across brain structures, life history and costs of neural tissue. However, when constraints also act on overall brain size, heterogeneity in selection across brain structures will favour region specific, or mosaic, evolution. Regardless, the respective advantages of developmentally coupled and uncoupled brain architectures mean that both may persist in fluctuating environments. This implies that developmental coupling is unlikely to be a persistent constraint, but could evolve as an adaptive outcome to selection to maintain functional integration.

Balance and constraint in revision TKR: A classification for instability management

Instability is an increasingly common cause and symptom of failure of Total Knee Arthroplasty (TKA). Patients seek 'Functional Stability', which is the sum of both a balanced joint and, if necessary, mechanical constraint. The objective of this paper is to classify the different types of TKA instability and their causes. Based on this classification, the authors give methodical recommendations for instability management.

Instability classification

Instability in revision TKA can be classified into 3 types based on the management of bone loss and ligamentous deficiency which directs the level of constraint required to achieve functional stability.

Type 1

Bone deficiency: Revision with restoration of joint line and rebuilding the bony anatomy results in a balanced joint. No increased constraint is needed.

Type 2

Ligament and soft tissue deficiency: Requires increased constraint to overcome instability.

Type 3

Composite (Total) deficiency: (combined Type 1 and 2).The multiple causes of instability are outlined for each Instability type along with an algorithm for restoring the joint line and adding titrated constraint to restore functional stability.

Interplay between personality and antisocial peer affiliation as prospective predictors of marijuana use and academic achievement in the transition into and out of college

Marijuana use has increased in recent cohorts and is associated with several negative outcomes, including poorer academic achievement. Less is known about how personality and peer factors in the first two years of college work together to predict problematic marijuana use and potentially co-occurring academic problems three years later. The longitudinal College Experiences Study (N = 209) was used to address this (N = 209, ~90% white, ~40% male); this study collected data from students in their first year of college, as well as ~1 year later (retention = 85%), and again ~4 years after the initial data collection (retention = 80%). Longitudinal data were analyzed via the traditional cross-lagged panel (CLPM) and the random-intercept CLPM approach. Results were consistent in that there was strong stability in problematic marijuana use, constraint, and antisocial peer affiliation across time, which were predominately influenced by stable, trait-like influences. These factors were also highly correlated but there was less evidence that one predicted the other over time. Nonetheless, greater constraint at Wave 1 was associated with significantly greater cumulative GPA in the transition out of college (βs = 0.43-0.44). Results support the importance of early prevention and intervention of problematic marijuana use, as well as the possibility of using personality-targeted approaches in the first year of college to promote growth in behaviors related to constraint (e.g., staying organized, risk avoidant) in an effort to improve academic success and correlated substance use outcomes by the transition out of college.

Economic analysis of the use of in vitro produced embryos transferred during heat stress under dairy herd constraints

The use of embryo transfer helps to improve reproductive performance during periods of heat stress. In vitro produced embryo transfer (IVP-ET) is more expensive than artificial insemination. We hypothesized that the value IVP-ET in seasonal herds depends on herd constraints, such as the maximum number of milking cows and the maximum number of calvings that can be accommodated throughout the year. Therefore, the objective of this study was to estimate how profitability in dairy herds exposed to summer heat stress is affected by the number of months in which IVP-ET is used, the use of IVP-ET in repeat-breeder cows, IVP-ET cost, and herd constraints. We built and used a nonlinear programming model of a dairy herd with young stock and cows with monthly Markov Chain transitions. The model varied the number of heifers calving in each calendar month to maximize herd profitability. We varied IVP-ET cost ($100 or $200), duration of the IVP-ET program (2 or 4 months), and the breeding number in which IVP-ET started (1st or 3rd). In total, 20 scenarios were simulated. Maximum profitability was obtained when IVP-ET was not used, regardless of herd constraints. The 16 scenarios in which IVP-ET was used showed increased seasonality in milk yield, numbers of milking cows, total cows, total calvings, and heifer calvings because the program tried to limit the number of IVP-ET breedings in the summer. The addition of the calving constraint increased the value of IVP-ET. The breakeven cost per IVP-ET ranged from -$6.79 to $24.38 compared with conventional semen cost of $20. In conclusion, the current market costs of IVP-ET did not warrant application with the objective to increase reproductive performance during heat stress. Herd constraints on the maximum allowable seasonality in the monthly number of milking cows and calvings affected the value of IVP-ET during heat stress.

TKA-Revision with maintenance of well-fixed metaphyseal sleeves: Indications and surgical technique

Due to the compromised bone situation revision implants need extended fixation options in order to achieve good long-term survival. Over decades this has been achieved with stems, either cemented or uncemented. In the last decade additional fixation options in terms of cementless metaphyseal sleeves or metaphyseal cones have been introduced and widely accepted. Revision of such implants is challenging, in particular if those porous coated parts are well integrated. Therefore, partial revision leaving the well-fixed parts in place can be an option if the indication is allowing it. This can help to preserve bone. In this study we show 2 cases with metaphyseal sleeves, in which we demonstrate when and how revision can be performed leaving sleeves in place. Meticulous pre-Op analysis of the failure mechanism is mandatory to find those few cases in which a partial revision can be recommended. In our cases, it was one patient with persistent tibia stem pain and another patient with secondary instability. In both cases implant fixation was not the problem, and therefore leaving the well-fixed sleeves in place was considered. Before final decision was made, specific information on implants sizes and constraint are needed. In our tibial revision stem thickness was less than 14 mm decision, in this situation the stem can be removed through the sleeve, leaving the sleeve in place. The technique how to do it, is shown in this study. In the second case a traumatic MCL rupture was leading to a secondary instability, needing a revision from a VVC constraint to a rotating hinge. Again, pre-Op analysis and the surgical technique of femoral component removal are described. In the great majority of cases a full revision with complete implant removal is required. In a few cases a partial revision with maintenance of implant parts can be considered but only after careful analysis of the failure mode. Even if the failure mode allows a partial revision specific implant information need to be obtained to clarify whether it is really possible. If it is possible, a specific surgical technique is recommended and described in this study.

Options and limitations of implant constraint

With an ever-increasing number of revisions, the surgeons will be faced with the dilemma of choosing the right implant for the revision knee. The soft tissue viability governs the choice of an implant at the time of revision. The selection ranges from the cruciate-retaining to the rotating/fixed hinge implants. The surgeon needs to plan preoperatively, but usually, the final decisions are made intraoperative. As determining the amount of constraint necessary can be challenging, we have tried to lay down a few pointers, which would help to make that choice. The posterior stabilized implants can manage most revision knees; in certain situations where they cannot accommodate the flexion-extension gap imbalance, a varus-valgus constrained implant should be used. The rotating hinge implants are used for severe instabilities or loss of soft tissue or bone around the knee. The use of a higher constraint implant has its consequences like reduced life span and reduced function. Thus it is crucial to use the least amount of constraint as necessary - however, as much as required.

Genetic correlations in the rhesus macaque dentition

Quantitative genetic analyses can indicate how complex traits respond to natural selection by demonstrating the genetic relationships between features that constrain their evolution. Genetic correlations between dental measurements have been estimated previously in baboons, humans, and tamarins and indicate variable patterns of modularity by tooth type across these taxa. Here, heritabilities of, and genetic correlations between, linear dental measurements were estimated from the Cayo Santiago rhesus macaques (Macaca mulatta). Relationships between the genetic correlation matrix and matrices designed to test hypotheses of modularity by tooth type, region, function, and development were assessed using a random skewers approach. Dental measurements were found to be moderately to highly heritable, with 24 of 28 heritability estimates differing significantly (p < 0.05) from zero. Almost all genetic correlations between dental dimensions were positive. The genetic correlation matrix was most similar to a regionally modular matrix, with distinct anterior and postcanine tooth modules. This pattern is consistent with previous quantitative genetic analyses of baboons and previous phenotypic analyses of cercopithecoid primates. The existence of a genetic module for the canines and honing premolar was not supported. Ongoing selection pressures, rather than strong genetic constraints, are likely necessary to preserve functional relationships between the canines and honing premolar based on these findings. The genetic correlation matrix of the Cayo Santiago rhesus macaques mirrors patterns of phenotypic correlations observed for cercopithecoid primates broadly and demonstrates that genetic contributions to these patterns may be fairly stable over the course of cercopithecoid evolution. The quantitative genetic study of additional taxa will be necessary to determine whether the regional modularity of baboons and macaques, or the integrated pattern of humans and tamarins, is shared more broadly across primates.

Which one restores in vivo knee kinematics effectively-medial or lateral pivot?

INTRODUCTION

Total knee arthroplasty (TKA) usually provides good pain relief and improved function but has generally been unable to fully restore normal knee kinematics. Does Medial or Lateral Pivot TKA designs guide us to native knee kinematics needs to be elucidated?

METHODS

Kinematic assessment of 13 knees with Medial Pivot TKA and 13 knees with Lateral Pivot TKA was done. The subjects were asked to perform step-up and weight bearing deep knee bend exercise under fluoroscopy for kinematic assessment. Patellar Tendon Angle (PTA) was measured after correcting f luoroscopic images for distortion against Knee Flexion Angle (KFA).

RESULTS

During the weight bearing deep knee bend, the average active maximum flexion achieved with Medial Pivot design was 113.8 ͦ as compared to 102.9 ͦ with Lateral Pivot design. There was no significant difference in PTA in step up and deep knee bend exercise between both the designs.

CONCLUSION

The kinematic assessment of both the Medial and Lateral Pivot TKA designs revealed linear trend of PTA with increasing KFA as described for normal knee. Both the designs were able to achieve functional knee range of motion.

Aligning functional network constraint to evolutionary outcomes

BACKGROUND

Functional constraint through genomic architecture is suggested to be an important dimension of genome evolution, but quantitative evidence for this idea is rare. In this contribution, existing evidence and discussions on genomic architecture as constraint for convergent evolution, rapid adaptation, and genic adaptation are summarized into alternative, testable hypotheses. Network architecture statistics from protein-protein interaction networks are then used to calculate differences in evolutionary outcomes on the example of genomic evolution in yeast, and the results are used to evaluate statistical support for these longstanding hypotheses.

RESULTS

A discriminant function analysis lent statistical support to classifying the yeast interactome into hub, intermediate and peripheral nodes based on network neighborhood connectivity, betweenness centrality, and average shortest path length. Quantitative support for the existence of genomic architecture as a mechanistic basis for evolutionary constraint is then revealed through utilizing these statistical parameters of the protein-protein interaction network in combination with estimators of protein evolution.

CONCLUSIONS

As functional genetic networks are becoming increasingly available, it will now be possible to evaluate functional genetic network constraint against variables describing complex phenotypes and environments, for better understanding of commonly observed deterministic patterns of evolution in non-model organisms. The hypothesis framework and methodological approach outlined herein may help to quantify the extrinsic versus intrinsic dimensions of evolutionary constraint, and result in a better understanding of how fast, effectively, or deterministically organisms adapt.

Individual variation of the masticatory system dominates 3D skull shape in the herbivory-adapted marsupial wombats

Background

Within-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses – particularly those produced through mastication of tough food items – may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the individual. In such cases, allometry may not dominate within-species shape variation, even if it is a driver of evolutionary shape divergence; ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus); but this main variation should emerge from high individual variability and thus have low eigenvalues.

Results

We assessed the evidence for high individual variation through 3D geometric morphometric shape analysis of crania and mandibles of three species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in individuals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between individual and ordinated shape variation was limited, indicating high levels of individual variability in the masticatory apparatus.

Discussion

Our results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that individual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraints act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.

Provision of Organ at Risk Contouring Guidance in UK Radiotherapy Clinical Trials

AIMS

Accurate delineation of organs at risk (OAR) is vital to the radiotherapy planning process. Inaccuracies in OAR delineation arising from imprecise anatomical definitions may affect plan optimisation and risk inappropriate dose delivery to normal tissues. The aim of this study was to review the provision of OAR contouring guidance in National Institute of Health Research Clinical Research Network (NIHR CRN) portfolio clinical trials.

MATERIALS AND METHODS

The National Radiotherapy Quality Trials Assurance (RTTQA) Group carried out a two-round Delphi assessment to determine which OAR descriptions provided optimal guidance.

RESULTS

Eighty-four clinical trials involving radiotherapy quality assurance were identified as either in recruitment or in setup within the NIHR CRN portfolio. Fifty-nine trials mandated OAR contouring. In total there were 412 OAR; 171 were uniquely named; 159 OAR had more than one name associated with a single structure, with the greatest nomenclature variation seen for the femoral head ± neck, the parotid gland, and bowel. The two-round Delphi assessment determined 42 OAR descriptions as providing optimal contouring guidance.

CONCLUSIONS

This study identified the need for OAR nomenclature and contouring guidance consistency across clinical trials. In response to this study and in conjunction with the Global Quality Assurance of Radiation Therapy Clinical Trials Harmonisation Group, the RTTQA Group is in collaboration with international partners to provide consensus recommendations for OAR delineation in clinical trials.

Transcending Therapy Models and Managing Complexity: Suggestions from Integrative Systemic Therapy

Integrative Systemic Therapy (IST) is a metatheoretical perspective for the conduct of individual, couple, and family therapy. Following a brief description of IST, this article presents developments in IST and their implication for psychotherapy integration. The nature of problem solving in IST is clarified, and the relationship between IST's essential problem-solving tasks and its core decision-making process is defined. Particular attention is paid to two dimensions of IST that have given it its name: integration and systems theory. The advantages of a therapy that is client system-centered and not model-driven are discussed, and a justification for "good enough" execution of interventions abstracted from specific models is provided. A procedure for balancing pragmatic demands of therapy with a commitment to account, as needed, for broader or deeper systemic issues is presented.

Rotating hinge knee causes lower bone-implant interface stress compared to constrained condylar knee replacement

PURPOSE

To compare the stresses at bone-arthroplasty interface of constrained and semi-constrained knee prostheses, using the finite element (FE) method as a predictor of the survivorship of the implants.

METHODS

Three-dimensional FE models of the knee implanted with rotating hinge (RHK) and legacy constrained condylar (LCCK) prostheses were generated to study the loads and stresses for two situations: medial- and lateral collateral ligament deficiencies in full extension.

RESULTS

On average, the shear stress developed at bone-implant interface dropped from 16.9 to 13.7 MPa (18.9%), and the interface von Mises stress lowered from 37.6 to 30.2 MPa (19.6%) in RHK compared to those in LCCK prostheses. RHK design also resulted in a more uniform stress distribution at the interfaces in both femur and tibia. The average polyethylene liner stress dropped from 9.6 to 2.6 MPa (a 72.7% decrease) in RHK design when compared to that in LCCK design.

CONCLUSION

The more uniform interface stress suggests fewer density changes at the periprosthetic regions due to bone remodelling. Moreover, the lower polyethylene stresses are likely to reduce wear and damage. These findings reveal that the RHK design may have more favorable mechanical features compared to LCCK design in full extension boundary conditions, implying a potentially better survivorship. However, the findings should be interpreted cautiously as other configurations were not investigated.

Key personality traits and alcohol use disorder symptoms in first and second year college students: detangling antecedent from consequence

BACKGROUND

Studies have consistently shown that low constraint and high negative emotionality are associated with higher levels of alcohol use and greater alcohol related problems. Less research has examined associations between these traits and alcohol use disorder (AUD) from the first to second year of college, when alcohol use increases rapidly, or has evaluated gender differences in these associations.

METHODS

The longitudinal College Experiences Study (N = 209, 60% female, 90% white) was used to detangle antecedent vs. consequence between constraint, negative emotionality, and AUD symptoms using multiple methods (cross-lagged panel analysis, latent difference score approach).

RESULTS

Providing evidence for a scar/complication model, greater AUD symptoms in the first year of college was predictive of rank-order and correlated decreases in constraint in the second year, but only for males. Surprisingly, negative emotionality was not associated with AUD symptoms for either gender. Qualitative analyses show that the vast majority of those that met an AUD diagnosis (90%+) did not consider their drinking to be problematic.

CONCLUSION

Given the vast majority of college students with AUD do not perceive their drinking to be problematic, results support the potential of using personality-based risk prevention/intervention programs to target at-risk individuals for problematic drinking, rather than targeting problematic drinking alone.

Agency and social constraint among victims of domestic minor sex trafficking: A method for measuring free will

Human agency has been a focus of philosophical and sociological concern from early debates about "free will" to recent themes in poststructuralism. Debates over the proper understanding of structure, agency, and constraint are hindered by the fact that few if any empirical measures of these concepts have been proposed. As sociologists have long recognized, the total results of the decisions of a group's members can be viewed as a distribution, and parameters can be fit to obtain a description of observed distributions. Here we propose the use of negative binomial curve to model population survival outcomes, and suggest that the parameters of such a curve represent reasonable surrogates for measures of agency, opportunity, and constraint when the decision process can be thought of as akin to a Bernoulli process. To provide an illustration of this approach, we discuss participation of legal minors in commercial sex (commonly referred to as victims of domestic minor sex trafficking (VDMST) or commercially sexually exploited children (CSEC)). In popular and advocacy-based accounts, considerable focus has been placed on the relative powerlessness of female VDMST. Using the proposed modeling technique, we test the extent to which male versus female VDMST appear to possess greater agency (or function under more limiting constraint) when deciding whether to remain in sex work or "leave the life". Contrary to existing literature, our results indicate that male and female underage sex workers are experiencing similar levels of agency, and differ mainly in opportunity, and constraint. Other individual circumstances are shown to contribute to varying levels of agency and constraint among sex workers, including street work status, community trouble, drug use, and the availability of an alternative income.

Factors affecting the choice of constrained prostheses when performing revision total knee arthroplasty

PURPOSE

The purposes of the present study were to assess the levels of prosthetic constraint chosen during revision total knee arthroplasty (TKA) and to identify factors influencing the choice of a constrained prosthesis.

METHODS

We retrospectively reviewed data on 274 revision TKAs. The mean follow-up period after revision TKA was 7.2 years. The femorotibial angle (FTA), joint line height (JLH), and Insall-Salvati ratio (ISR) were radiographically evaluated. Factors affecting the extent of constraint chosen were evaluated in terms of age, gender, body mass index, primary diagnosis, the cause of revision TKA, the Anderson Orthopedic Research Institute (AORI) classification, and changes in the JLH and ISR.

RESULTS

Totals of 247 (90.1%), 11 (4.0%), and 9 (3.4%) knees received posteriorly stabilized prostheses, constrained condylar knees, and rotating hinge prostheses, respectively. On multivariate analysis, the cause of revision TKA including loosening and instability and the changes in the JLH and ISR affected independently the choice of a constrained prosthesis.

CONCLUSIONS

The frequency of implantation of constrained prostheses was 7.4% in the present study. Consideration of various factors including the cause of revision TKA and changes in the JLH and ISR will aid the TKA surgeon in selecting prostheses with appropriate constraints when performing revision TKAs.

The linguistic constraint on contraction in children with SLI

PURPOSE

The goal of the present study was to investigate whether children with specific language impairment (SLI) obey the constraint on contraction with the verb BE in three linguistic contexts: ellipsis, yes/no questions and embedded questions.

METHOD

Using elicited production methodology, a total of 51 children were tested: 17 children with SLI (mean age = 5;6); 17 language-matched children matched on mean length of utterance (mean age = 3;6) and 17 children age-matched children (mean age = 5;4).

RESULTS

The experimental results revealed that children with SLI did not differ from the children in the control groups. Children contracted BE where it is possible and failed to contract in the linguistic contexts where contraction is prohibited. Our experimental findings suggest that for this aspect of linguistic knowledge children with SLI have the same underlying grammar as children whose grammars are typically-developing.

Nearly 200 years of sustained selection have not overcome the leaf area-stem size relationship in the poinsettia

Organismal parts often covary in their proportions, a phenomenon known as allometry. One way of exploring the causes of widespread allometric patterns is with artificial selection, to test whether or not it is possible to move populations into "empty" allometric space not occupied by the wild type. Domesticated organisms have been subject to many generations of selection, making them ideal model systems. We used the domesticated Christmas poinsettia Euphorbia pulcherrima in combination with wild populations to examine the origin of the proportionality between leaf area and stem size, which scales predictably across nearly all plants. In accordance with the stated aims of breeders to produce more compact plants, we predicted that domesticated poinsettias would have greater leaf area for a given stem volume than the tall, lanky wild ancestors. Our data rejected this prediction, showing instead that domesticates have leaf area-stem volume relationships identical to the wild ancestors. Presumably the metabolic dependence between stems and leaves makes the leaf area-stem volume relationship difficult to overcome. The relative fixity of this relationship leads to predictable covariation in other traits: The fuller outlines of domestic poinsettias involve significantly shorter internodes, and given a constant leaf area-stem volume relationship, smaller individual leaf areas. At the same time, domestic poinsettias are subject to selection favoring breakage resistance, which is achieved via thicker stems for a given length rather than stiffer stem tissue resistance to bending. Our results show that domesticated poinsettias differ from wild plants in a suite of traits including leaf size, internode distances, and stem length-diameter relations, but despite over 200 years of selection favoring rounded outlines, there has been no change in the total leaf area-stem volume relationship, helping to predict which changes are likely achievable and which will not be under continued artificial selection and in the wild.

External biomechanical constraints impair maximal voluntary grip force stability post-stroke

BACKGROUND

Grip strength is frequently measured as a global indicator of motor function. In clinical populations, such as hemiparesis post-stroke, grip strength is associated with upper-extremity motor impairment, function, and ability to execute activities of daily living. However, biomechanical configuration of the distal arm and hand may influence the magnitude and stability of maximal voluntary grip force and varies across studies. The influence of distal arm/hand biomechanical configuration on grip force remains unclear. Here we investigated how biomechanical configuration of the distal arm/hand influence the magnitude and trial-to-trial variability of maximal grip force performed in similar positions with variations in external constraint.

METHODS

We studied three groups of 20 individuals: healthy young, healthy older, and individuals post-stroke. We tested maximal voluntary grip force in 4 conditions: 1: self-determined/"free"; 2: standard; 3: fixed arm-rest; 4: gripper fixed to arm-rest, using an instrumented grip dynamometer in both dominant/non-dominant and non-paretic/paretic hands.

FINDINGS

Regardless of hand or group, maximal voluntary grip force was highest when the distal limb was most constrained (i.e., Condition 4), followed by the least constrained (i.e., Condition 1) (Cohen's f = 0.52, P's < 0.001). Coefficient of variation among three trials was greater in the paretic hand compared with healthy individuals, particularly in more (Conditions 3 and 4) compared to less (Conditions 1 and 2) constrained conditions (Cohen's f = 0.29, P's < 0.05).

INTERPRETATION

These findings have important implications for design of rehabilitation interventions and devices. Particularly in individuals post-stroke, external biomechanical constraints increase maximal voluntary grip force variability while fewer biomechanical constraints yield more stable performance.

Homeotic transformations reflect departure from the mammalian 'rule of seven' cervical vertebrae in sloths: inferences on the Hox code and morphological modularity of the mammalian neck

Background

Sloths are one of only two exceptions to the mammalian ‘rule of seven’ vertebrae in the neck. As a striking case of breaking the evolutionary constraint, the explanation for the exceptional number of cervical vertebrae in sloths is still under debate. Two diverging hypotheses, both ultimately linked to the low metabolic rate of sloths, have been proposed: hypothesis 1 involves morphological transformation of vertebrae due to changes in the Hox gene expression pattern and hypothesis 2 assumes that the Hox gene expression pattern is not altered and the identity of the vertebrae is not changed. Direct evidence supporting either hypothesis would involve knowledge of the vertebral Hox code in sloths, but the realization of such studies is extremely limited. Here, on the basis of the previously established correlation between anterior Hox gene expression and the quantifiable vertebral shape, we present the morphological regionalization of the neck in three different species of sloths with aberrant cervical count providing indirect insight into the vertebral Hox code.

Results

Shape differences within the cervical vertebral column suggest a mouse-like Hox code in the neck of sloths. We infer an anterior shift of HoxC-6 expression in association with the first thoracic vertebra in short-necked sloths with decreased cervical count, and a posterior shift of HoxC-5 and HoxC-6 expression in long-necked sloths with increased cervical count.

Conclusion

Although only future developmental analyses in non-model organisms, such as sloths, will yield direct evidence for the evolutionary mechanism responsible for the aberrant number of cervical vertebrae, our observations lend support to hypothesis 1 indicating that the number of modules is retained but their boundaries are displaced. Our approach based on quantified morphological differences also provides a reliable basis for further research including fossil taxa such as extinct ‘ground sloths’ in order to trace the pattern and the underlying genetic mechanisms in the evolution of the vertebral column in mammals.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1202-5) contains supplementary material, which is available to authorized users.

Pre-clinical assessment of total knee replacement anterior-posterior constraint

Pre-clinical, bench-top assessment of Total Knee Replacements (TKR) can provide information about the inherent constraint provided by a TKR, which does not depend on the condition of the patient undergoing the arthroplasty. However little guidance is given by the ASTM standard on test configurations such as medial-lateral (M:L) loading distribution, flexion angle or restriction of secondary motions. Using a purpose built rig for a materials testing machine, four TKRs currently in widespread clinical use, including medial-pivot and symmetrical condyle types, were tested for anterior-posterior translational constraint. Compressive joint loads from 710 to 2000 N, and a range of medial-lateral (M:L) load distributions, from 70:30% to 30:70% M:L, were applied at different flexion angles with secondary motions unconstrained. It was found that TKA constraint was significantly less at 60 and 90° flexion than at 0°, whilst increasing the compressive joint load increased the force required to translate the tibia to limits of AP constraint at all flexion angles tested. Additionally when M:L load distribution was shifted medially, a coupled internal rotation was observed with anterior translation and external rotation with posterior translation. This paper includes some recommendations for future development of pre-clinical testing methods.

Understanding environmental sounds in sentence context

There is debate about how individuals use context to successfully predict and recognize words. One view argues that context supports neural predictions that make use of the speech motor system, whereas other views argue for a sensory or conceptual level of prediction. While environmental sounds can convey clear referential meaning, they are not linguistic signals, and are thus neither produced with the vocal tract nor typically encountered in sentence context. We compared the effect of spoken sentence context on recognition and comprehension of spoken words versus nonspeech, environmental sounds. In Experiment 1, sentence context decreased the amount of signal needed for recognition of spoken words and environmental sounds in similar fashion. In Experiment 2, listeners judged sentence meaning in both high and low contextually constraining sentence frames, when the final word was present or replaced with a matching environmental sound. Results showed that sentence constraint affected decision time similarly for speech and nonspeech, such that high constraint sentences (i.e., frame plus completion) were processed faster than low constraint sentences for speech and nonspeech. Linguistic context facilitates the recognition and understanding of nonspeech sounds in much the same way as for spoken words. This argues against a simple form of a speech-motor explanation of predictive coding in spoken language understanding, and suggests support for conceptual-level predictions.

Combined Intracapsular And Extracapsular Neck Of Femur Fractures Case Series, Literature Review And Management Recommendations

Concomitant ipsilateral intracapsular and extracapsular fractures of the femoral neck are rare injuries with only 14 cases described in the literature as single case reports. We present three cases that were successfully and uniquely treated by uncemented hip arthroplasties. Two patients underwent complex primary uncemented total hip replacements, and one patient underwent an uncemented bipolar fluted stem hemiarthroplasty. The level of bearing constraint varied between implants. After describing our cases we review the literature and make recommendations on the management of these injuries. We believe that these are significant injuries and best functional results can be achieved with an early diagnosis and patient-specific approach that can include a total hip replacement in appropriate cases.

Changes in anteroposterior stability and proprioception after different types of knee arthroplasty

PURPOSE

To compare different types of knee arthroplasty, in selected patients with a knee score above 80 points, for their post-operative changes in anteroposterior (AP) laxity and proprioception.

METHODS

Four groups of each ten patients were tested for AP translation after different types of arthroplasty with a KT-1000 device at 30°, 60° and 90° of flexion. Proprioception of the joint was evaluated by joint position sense with three different tests. Clinical outcome of stability and proprioceptive testing was analysed by comparing the results of three (KSS, KOOS and FJS-12) patient-reported outcome measurement scores (PROMS) for each of the different implant types.

RESULTS

Anteroposterior laxity was observed at 30° and 90° of flexion for the two PS TKA designs included in this study, but not for the UKA or the medial pivot design. All knee designs, except UKA, had an increased laxity at 60° of flexion. Proprioceptive testing was inconclusive. PROMS were not able to identify differences in clinical outcome among different knee designs in these selected patients, despite observed differences in AP laxity.

CONCLUSION

Increased AP laxity is a result of the surgical procedure in knee arthroplasty. UKA is the only design mimicking native laxity of the knee. A medial pivot design can obtain the same result as UKA at 30° and 90° of flexion, but not at the importantly cited 60° of flexion as tested under non-load-bearing conditions. The clinical relevance of this study is that despite of an important range of AP translations among the different knee designs, good-to-excellent patient-reported outcome was observed within the findings of this study.

LEVEL OF EVIDENCE

II.

Constraining movement reveals motor capability in chronic stroke: an initial study

OBJECTIVE

To determine if persons with chronic stroke and decreased hip and knee flexion during swing can walk with improved swing-phase kinematics when the task demands constrained gait to the sagittal plane.

DESIGN

A one-day, within-subject design comparing gait kinematics under two conditions: Unconstrained treadmill walking and a constrained condition in which the treadmill walking space is reduced to limit limb advancement to occur in the sagittal plane.

SETTING

Outpatient physical therapy clinic.

SUBJECTS

Eight individuals (mean age, 64.1 ±9.3, 2 F) with mild-moderate paresis were enrolled.

MAIN MEASURES

Spatiotemporal gait characteristics and swing-phase hip and knee range of motion during unconstrained and constrained treadmill walking were compared using paired t-test and Cohen's d ( d) to determine effect size.

RESULTS

There was a significant, moderate-to-large effect of the constraint on hip flexion ( p < 0.001, d = -1.1) during initial swing, and hip ( p < 0.05, d = -0.8) and knee ( p < 0.001, d = -1.1) flexion during midswing. There was a moderate effect of constraint on terminal swing knee flexion ( p = 0.238, d = -0.6). Immediate and significant changes in step width ( p < 0.05, d = 0.9) and paretic step length ( p < 0.05, d = -0.5) were noted in the constrained condition compared with unconstrained.

CONCLUSION

Constraining the treadmill walking path altered the gait patterns among the study's participants. The immediate change during constrained walking suggests that patients with chronic stroke may have underlying movement capability that they do not preferentially utilize.

Constraint is associated with earlier circadian phase and morningness: Confirmation of relationships between personality and circadian phase using a constant routine protocol

Associations among personality, diurnal preference, and circadian phase were investigated using a constant routine laboratory protocol. One hundred and sixty-eight healthy participants aged 18-30 years (Women n = 68) completed either a 30- or 50-hour constant routine under dim-light conditions (<3 lux), during which circadian phase was measured from core body temperature and melatonin. Prior to laboratory admission, self-report measures of personality and diurnal preference were also obtained. The personality trait of Constraint correlated positively with morning diurnal preference and earlier circadian phase, with circadian phase partially mediating the relationship between Constraint and diurnal preference. No other personality variables correlated with circadian phase. Sex was an important covariate in several of the relationships investigated due to lower levels of Constraint and later CBT phase amongst men and was thus controlled for in all relevant analyses. Findings from this highly controlled study are consistent with previous field research in suggesting that earlier circadian phase is associated with the personality trait of Constraint.

Normal personality traits, rumination and stress generation among early adolescent girls

This study examined associations between personality and stress generation. Expanding upon prior work, we examined (a) the role of Positive Emotionality (PE), Negative Emotionality (NE), and Constraint (CON), and their lower-order facets, as predictors of acute and chronic interpersonal stress generation; (b) whether personality moderated effects of rumination on stress generation; and (c) whether personality increased exposure to independent (uncontrollable) stress. These questions were examined in a one-year study of 126 adolescent girls (M age = 12.39 years) using contextual stress interviews. NE predicted increases in acute and chronic interpersonal stress generation, but not independent stress. NE, CON and affiliative PE each moderated the effect of rumination on chronic interpersonal stress generation. These effects were driven by particular lower-order traits.

On the meaning of chance in biology

Chance has somewhat different meanings in different contexts, and can be taken to be either ontological (as in quantum indeterminacy) or epistemological (as in stochastic uncertainty). Here I argue that, whether or not it stems from physical indeterminacy, chance is a fundamental biological reality that is meaningless outside the context of knowledge. To say that something happened by chance means that it did not happen by design. This of course is a cornerstone of Darwin's theory of evolution: random undirected variation is the creative wellspring upon which natural selection acts to sculpt the functional form (and hence apparent design) of organisms. In his essay Chance & Necessity, Jacques Monod argued that an intellectually honest commitment to objectivity requires that we accord chance a central role in an otherwise mechanistic biology, and suggested that doing so may well place the origin of life outside the realm of scientific tractability. While that may be true, ongoing research on the origin of life problem suggests that abiogenesis may have been possible, and perhaps even probable, under the conditions that existed on primordial earth. Following others, I argue that the world should be viewed as causally open, i.e. primordially indeterminate or vague. Accordingly, chance ought to be the default scientific explanation for origination, a universal 'null hypothesis' to be assumed until disproven. In this framework, creation of anything new manifests freedom (allowing for chance), and causation manifests constraint, the developmental emergence of which establishes the space of possibilities that may by chance be realized.

Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening

Docking-based virtual screening is an established component of structure-based drug discovery. Nevertheless, scoring and ranking of computationally docked ligand libraries still suffer from many false positives. Identifying optimal docking parameters for a target protein prior to virtual screening can improve experimental hit rates. Here, we examine protocols for virtual screening against the important but challenging class of drug target, protein tyrosine phosphatases. In this study, common interaction features were identified from analysis of protein-ligand binding geometries of more than 50 complexed phosphatase crystal structures. It was found that two interactions were consistently formed across all phosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least one interaction with the P-loop backbone amide. In order to investigate the significance of these features on phosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on three phosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine and P-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of the virtual screen significantly increased in the three studied phosphatases, by up to a factor of two in some cases. Additionally, the use of such pharmacophoric constraints considerably improved the ability of docking to predict the inhibitor's bound pose, decreasing RMSD to the crystallographic geometry by 43% on average. Constrained docking improved enrichment of screens against both open and closed conformations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found to generally improve enrichment. The knowledge-based computational strategies explored here can potentially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening.

On the findability of genotypes

Can we define a measure that describes how easy or difficult it is for a population to evolve to a specific genotype? For populations evolving under weak mutation on a time-invariant fitness landscape, I argue that one appropriate measure is the expected waiting time, starting from equilibrium, for a population to become fixed for a given genotype. Under this definition for the "findability" of genotypes, I show that for any pair of genotypes (1) a population at equilibrium is always more likely to fix at the more findable before the less findable genotype and (2) the expected time to evolve from the more findable to the less findable genotype is always greater that the expected time to evolve in the opposite direction. Although increasing the fitness of a genotype always increases its findability, in general there is no simple relationship between the rank ordering of genotypes by fitness and the rank ordering of genotypes by findability. I also present a method for quantifying the relative contributions of mutation, selection, substitution rate, and probability of reversion to a genotype's findability.

Age-independent effects of pubertal status on behavioral constraint in healthy adolescents

Studies have examined age-related changes in personality traits from adolescence through young adulthood, finding that aspects of negative emotionality decrease while conscientiousness increases over time. Varied mechanisms may underlie these transitions, including puberty-driven hormonal changes. Here, healthy adolescents completed the Multidimensional Personality Questionnaire-Brief Form and self-report measures of pubertal status at baseline and after two years. Independent of age, pubertal status impacted primary trait scales of the MPQ-BF Constraint factor in a sex-specific manner. Females decreased in Constraint, and particularly Control, while males increased in Constraint, and particularly Harm Avoidance, with advancing puberty. Longitudinal analyses validated these findings for Control. Findings are discussed relative to males' versus females' achievement of optimal levels of behavioral control in adolescence.