Contactin 2 homophilic adhesion structure and conformational plasticity

The cell-surface attached glycoprotein contactin 2 is ubiquitously expressed in the nervous system and mediates homotypic cell-cell interactions to organize cell guidance, differentiation, and adhesion. Contactin 2 consists of six Ig and four fibronectin type III domains (FnIII) of which the first four Ig domains form a horseshoe structure important for homodimerization and oligomerization. Here we report the crystal structure of the six-domain contactin 2Ig1-6 and show that the Ig5-Ig6 combination is oriented away from the horseshoe with flexion in interdomain connections. Two distinct dimer states, through Ig1-Ig2 and Ig3-Ig6 interactions, together allow formation of larger oligomers. Combined size exclusion chromatography with multiangle light scattering (SEC-MALS), small-angle X-ray scattering (SAXS) and native MS analysis indicates contactin 2Ig1-6 oligomerizes in a glycan dependent manner. SAXS and negative-stain electron microscopy reveals inherent plasticity of the contactin 2 full-ectodomain. The combination of intermolecular binding sites and ectodomain plasticity explains how contactin 2 can function as a homotypic adhesion molecule in diverse intercellular environments.

Imaging features of renal ectopia and fusion in 13 cats

CASE SERIES SUMMARY

A retrospective multicenter case series of renal fusion anomalies in cats was investigated. The aim of this study was to describe the imaging characteristics (radiography, ultrasonography and CT) of renal ectopia and fusion in cats. A total of 13 feline patients (median age 9 years) were included in this multicentric retrospective study. Ultrasound was available in 12/13 cases, radiographs in 4/13 cases and CT in 3/13 cases. Of the 13 cases, seven were left to right fusions, four were right to left fusions, one was on the midline and one was in the pelvic inlet. Adopting a human classification system, there were five lump kidneys, four disc kidneys, one horseshoe kidney, one caudal ectopia, one L-shaped kidney and one pelvic kidney. In 2/13 cases, additional congenital malformations were noted, including an azygous continuation of the caudal vena cava and a peritoneal-pericardial diaphragmatic hernia.

RELEVANCE AND NOVEL INFORMATION

This study provides further description of the imaging findings in feline patients with fused renal ectopia. The morphologic characteristics of the fused kidneys in cats appear similar to what is published in the human literature. Renal fusion might be an incidental finding in cats, but further investigations are necessary to determine their clinical relevance.

Hoof Expansion, Deformation, and Surface Strains Vary with Horseshoe Nail Positions

Racehorses are susceptible to underrun heel hoof conformation. Racehorses are often shod with nails placed toward the heel. It is unknown if palmar nails restrict or alter hoof deformation in a manner that could promote the development of underrun heel conformation over time with repeated loading. To determine how the addition of palmar nails affects heel deformation during limb loading, hoof expansion and hoof wall deformations were quantified using rosette strain gauges and kinematic markers during in the vitro limb loading of cadaveric limbs that simulated midstance for walk, trot, and canter loads. Nail treatments used to attach a horseshoe to the hoof included: toe nails (T), toe and quarter nails (TQ), and toe, quarter, and heel nails (TQH). The effects of nail treatment on heel expansion and hoof wall deformations were assessed using repeated measures analysis of variance (p < 0.05). Nails placed palmar to the quarters of the hoof decreased heel expansion (p < 0.001). Heel nails resulted in the largest changes in hoof wall principal strain directions distally. The application of nails palmar to the hoof quarters alters hoof wall deformation during limb loading. The continued loading of the hoof with palmer nails could alter hoof conformation over time.

Bayesian Uncertainty Estimation for Gaussian Graphical Models and Centrality Indices

In the network approach to psychopathology, psychological constructs are conceptualized as networks of interacting components (e.g., the symptoms of a disorder). In this network view, interest is on the degree to which symptoms influence each other, both directly and indirectly. These direct and indirect influences are often captured with centrality indices, however, the estimation method often used with these networks, the frequentist graphical LASSO (GLASSO), has difficulty estimating (uncertainty in) these measures. Bayesian estimation might provide a solution, as it is better suited to deal with bias in the sampling distribution of centrality indices. This study therefore compares estimation of symptom networks with Bayesian GLASSO- and Horseshoe priors to estimation using the frequentist GLASSO using extensive simulations. Results showed that the Bayesian GLASSO performed better than the Horseshoe, and that the Bayesian GLASSO outperformed the frequentist GLASSO with respect to bias in edge weights, centrality measures, correlation between estimated and true partial correlations, and specificity. Sensitivity was better for the frequentist GLASSO, but performance of the Bayesian GLASSO is usually close. With respect to uncertainty in the centrality measures, the Bayesian GLASSO shows good coverage for strength and closeness centrality, but uncertainty in betweenness centrality is estimated less well.

Selecting relevant moderators with Bayesian regularized meta-regression

When meta-analyzing heterogeneous bodies of literature, meta-regression can be used to account for potentially relevant between-studies differences. A key challenge is that the number of candidate moderators is often high relative to the number of studies. This introduces risks of overfitting, spurious results, and model non-convergence. To overcome these challenges, we introduce Bayesian Regularized Meta-Analysis (BRMA), which selects relevant moderators from a larger set of candidates by shrinking small regression coefficients towards zero with regularizing (LASSO or horseshoe) priors. This method is suitable when there are many potential moderators, but it is not known beforehand which of them are relevant. A simulation study compared BRMA against state-of-the-art random effects meta-regression using restricted maximum likelihood (RMA). Results indicated that BRMA outperformed RMA on three metrics: BRMA had superior predictive performance, which means that the results generalized better; BRMA was better at rejecting irrelevant moderators, and worse at detecting true effects of relevant moderators, while the overall proportion of Type I and Type II errors was equivalent to RMA. BRMA regression coefficients were slightly biased towards zero (by design), but its residual heterogeneity estimates were less biased than those of RMA. BRMA performed well with as few as 20 studies, suggesting its suitability as a small sample solution. We present free open source software implementations in the R-package pema (for penalized meta-analysis) and in the stand-alone statistical program JASP. An applied example demonstrates the use of the R-package.

Pharmacogenetic Dose Modeling Based on CYP2C19 Allelic Phenotypes

Pharmacogenetic variability in drug metabolism leads to patient vulnerability to side effects and to therapeutic failure. Our purpose was to introduce a systematic statistical methodology to estimate quantitative dose adjustments based on pharmacokinetic differences in pharmacogenetic subgroups, addressing the concerns of sparse data, incomplete information on phenotypic groups, and heterogeneity of study design. Data on psychotropic drugs metabolized by the cytochrome P450 enzyme CYP2C19 were used as a case study. CYP2C19 activity scores were estimated, while statistically assessing the influence of methodological differences between studies, and used to estimate dose adjustments in genotypic groups. Modeling effects of activity scores in each substance as a population led to prudential predictions of adjustments when few data were available ('shrinkage'). The best results were obtained with the regularized horseshoe, an innovative Bayesian approach to estimate coefficients viewed as a sample from two populations. This approach was compared to modeling the population of substance as normally distributed, to a more traditional "fixed effects" approach, and to dose adjustments based on weighted means, as in current practice. Modeling strategies were able to assess the influence of study parameters and deliver adjustment levels when necessary, extrapolated to all phenotype groups, as well as their level of uncertainty. In addition, the horseshoe reacted sensitively to small study sizes, and provided conservative estimates of required adjustments.

Polycystic Horseshoe Kidney: A Rare Coexistence as a Challenge for the Surgeons. Case Report

Autosomal dominant polycystic kidney disease (ADPKD) with concomitant horseshoe kidney is an extremely rare entity. In this case, we report a 45-year-old male patient with ADPKD and a horseshoe kidney who demonstrated hypertension, urological complications, and discomfort symptoms such as pain, breathing difficulties, and abdominal meteorism. After preoperative assessment and planning, the patient underwent nephrectomy. Bilateral nephrectomy without dividing the isthmus was performed successfully. The isthmus, which had complicated vasculature and was full of cysts, remained intact, avoiding severe bleeding and infection. The postoperative course was uneventful. Keeping the isthmus intact in such cases is a challenge for the surgeon. The rarity of polycystic horseshoe kidney in combination with the altered abdominal anatomy requires the proper preoperative strategy in order to avoid intraoperative complications.

Identifying treatment effect heterogeneity in dose-finding trials using Bayesian hierarchical models

An important task in drug development is to identify patients, which respond better or worse to an experimental treatment. Identifying predictive covariates, which influence the treatment effect and can be used to define subgroups of patients, is a key aspect of this task. Analyses of treatment effect heterogeneity are however known to be challenging, since the number of possible covariates or subgroups is often large, while samples sizes in earlier phases of drug development are often small. In addition, distinguishing predictive covariates from prognostic covariates, which influence the response independent of the given treatment, can often be difficult. While many approaches for these types of problems have been proposed, most of them focus on the two-arm clinical trial setting, where patients are given either the treatment or a control. In this article we consider parallel groups dose-finding trials, in which patients are administered different doses of the same treatment. To investigate treatment effect heterogeneity in this setting we propose a Bayesian hierarchical dose-response model with covariate effects on dose-response parameters. We make use of shrinkage priors to prevent overfitting, which can easily occur, when the number of considered covariates is large and sample sizes are small. We compare several such priors in simulations and also investigate dependent modeling of prognostic and predictive effects to better distinguish these two types of effects. We illustrate the use of our proposed approach using a Phase II dose-finding trial and show how it can be used to identify predictive covariates and subgroups of patients with increased treatment effects.

A Simple Protocol to Effectively Manage Anal Fistulas with No Obvious Internal Opening

Purpose

In some anal fistulas, the internal/primary opening cannot be located even after examination and assessment on MRI or transrectal ultrasound. The efficacy of a simple new protocol to manage such therapeutically challenging fistulas was tested.

Patients and Methods

All anal fistula patients operated consecutively over 7 years were included in the study. A simple two-step protocol was followed for fistulas in which the internal opening was not locatable after clinical examination and MRI assessment. First, the MRI was reassessed. The site where the fistula was closest to the internal sphincter was noted. It was assumed that the internal-opening was located at that position and the fistula was treated accordingly. Second, in horseshoe anal fistulas with no apparent internal opening, it was assumed that the internal opening was located in the midline. Low fistulas were treated by fistulotomy and high fistulas by a sphincter-sparing procedure. Incontinence was evaluated by objective incontinence scores (Vaizey scores).

Results

A total of 757 patients were operated (median follow-up-33 months). Of these, 57 patients were excluded due to short or inadequate follow-up. In 154/700 (22%) patients, the internal opening could not be located while in 546/700 (78%), the internal opening was found. Both the groups were similar in all parameters. In the "internal-opening found" group, the fistula healed completely in 486/546 (89%) and in the 'internal-opening not found group', the fistula healed in 140/156 (90.9%) (p=1.01). The objective continence scores did not change significantly after surgery in both the groups.

Conclusion

This new protocol seems effective as a high cure rate could be achieved in 'internal-opening not found' fistulas which was comparable to fistula healing in the 'internal-opening found' group.

Management of Colon Perforation During Percutaneous Nephrolithotomy in Patients with Complex Anatomy: A Case Series

Percutaneous nephrolithotomy (PCNL), first described in 1976, is the gold standard for the management of large kidney stones, with stone-free rates as high as 95% in contemporary literature. Colonic injuries during PCNL are a rare complication with an estimated incidence of 0.3%-0.5%. However, given the high morbidity incurred and the necessity of prompt operative intervention, it is imperative that practitioners have a low suspicion threshold for such injuries, particularly in those patients with altered or complex anatomy. This case series addresses peri- and postoperative outcomes of colon perforation during PCNL in patients with complex anatomy and reviews the technical challenges of surgery with potential methods to avoid injury in the future. Herein we review three instances of colonic injuries and their subsequent management to highlight both the presentation and the optimal management of these rare occurrences.

Trot Accelerations of Equine Front and Hind Hooves Shod with Polyurethane Composite Shoes and Steel Shoes on Asphalt

The present study investigated accelerations of the front and hind hooves of horses comparing two different shoe types. A standard steel shoe, with studs, pins, and in some instances with toe grabs, was compared to a steel shoe covered on the bottom with a layer of polyurethane. Four horses were used; they trotted in hand on an asphalt track at their self-selected speed. The results showed significantly reduced decelerations during the stance phase with the polyurethane-covered shoes (10th percentile median steel -2.77 g, polyurethane -2.46 g; p = 0.06) and significantly increased decelerations in front hooves compared to hind hooves with steel shoes (70th percentile median -1.04 g front hooves, 0.12 g hind hooves, p = 0.04). Horses trotted faster using longer strides with the polyurethane-covered shoes compared to the steel shoes. The results show that effects of shoe types should be investigated simultaneously in front and hind hooves, and that PU shoes may aid in reducing the overload present in the front limbs of horses.

Changes in Hoof Shape During a Seven-Week Period When Horses Were Shod Versus Barefoot

This crossover study tested the hypothesis that hoof shape would differ after a seven-week period of horses (n = 11) wearing shoes versus barefoot. An ANOVA appropriate to a crossover design was used to assess the differences in the change in hoof shape over the seven-week period and significance was set at p < 0.05. Results are displayed as the mean difference for horses when shod versus barefoot ± the SEM for the left (L) and right (R) front hooves. Proximal hoof circumference (PHC) decreased when horses were shod and barefoot, but this decrease was greater when horses were shod (L -0.65 ± 0.16 cm; p = 0.0026; R -0.78 ± 0.13 cm; p = 0.0002). Hoof angle increased slightly when horses were barefoot and decreased when they were shod (L -1.70 ± 0.31°; p = 0.0004; R -1.84 ± 0.54°; p = 0.0079). Sole length decreased more when horses were barefoot, but this was only significant for the right fore (R 5.07 ± 1.06 mm; p = 0.0010). Solar circumference increased when horses were barefoot but decreased when shod (L -1.19 ± 0.41 cm; p = 0.0182; R -1.50 ± 0.31 cm; p = 0.0010). This is the first study to show a significantly lower PHC when horses were shod compared to barefoot. The study suggests that shod horses may benefit from a shorter shoeing interval to help mitigate the changes in hoof angle.

Bayesian data integration and variable selection for pan-cancer survival prediction using protein expression data

Accurate prognostic prediction using molecular information is a challenging area of research, which is essential to develop precision medicine. In this paper, we develop translational models to identify major actionable proteins that are associated with clinical outcomes, like the survival time of patients. There are considerable statistical and computational challenges due to the large dimension of the problems. Furthermore, data are available for different tumor types; hence data integration for various tumors is desirable. Having censored survival outcomes escalates one more level of complexity in the inferential procedure. We develop Bayesian hierarchical survival models, which accommodate all the challenges mentioned here. We use the hierarchical Bayesian accelerated failure time model for survival regression. Furthermore, we assume sparse horseshoe prior distribution for the regression coefficients to identify the major proteomic drivers. We borrow strength across tumor groups by introducing a correlation structure among the prior distributions. The proposed methods have been used to analyze data from the recently curated "The Cancer Proteome Atlas" (TCPA), which contains reverse-phase protein arrays-based high-quality protein expression data as well as detailed clinical annotation, including survival times. Our simulation and the TCPA data analysis illustrate the efficacy of the proposed integrative model, which links different tumors with the correlated prior structures.

Fabrication Approaches to Interconnect Based Devices for Stretchable Electronics: A Review

Stretchable electronics promise to naturalize the way that we are surrounded by and interact with our devices. Sensors that can stretch and bend furthermore have become increasingly relevant as the technology behind them matures rapidly from lab-based workflows to industrially applicable production principles. Regardless of the specific materials used, creating stretchable conductors involves either the implementation of strain reliefs through insightful geometric patterning, the dispersion of stiff conductive filler in an elastomeric matrix, or the employment of intrinsically stretchable conductive materials. These basic principles however have spawned a myriad of materials systems wherein future application engineers need to find their way. This paper reports a literature study on the spectrum of different approaches towards stretchable electronics, discusses standardization of characteristic tests together with their reports and estimates matureness for industry. Patterned copper foils that are embedded in elastomeric sheets, which are closest to conventional electronic circuits processing, make up one end of the spectrum. Furthest from industry are the more recent circuits based on intrinsically stretchable liquid metals. These show extremely promising results, however, as a technology, liquid metal is not mature enough to be adapted. Printing makes up the transition between both ends, and is also well established on an industrial level, but traditionally not linked to creating electronics. Even though a certain level of maturity was found amongst the approaches that are reviewed herein, industrial adaptation for consumer electronics remains unpredictable without a designated break-through commercial application.

Uncovering the Horseshoe Effect in Microbial Analyses

The horseshoe effect is often considered an artifact of dimensionality reduction. We show that this is not true in the case for microbiome data and that, in fact, horseshoes can help analysts discover microbial niches across environments.

The horseshoe effect is a phenomenon that has long intrigued ecologists. The effect was commonly thought to be an artifact of dimensionality reduction, and multiple techniques were developed to unravel this phenomenon and simplify interpretation. Here, we provide evidence that horseshoes arise as a consequence of distance metrics that saturate—a familiar concept in other fields but new to microbial ecology. This saturation property loses information about community dissimilarity, simply because it cannot discriminate between samples that do not share any common features. The phenomenon illuminates niche differentiation in microbial communities and indicates species turnover along environmental gradients. Here we propose a rationale for the observed horseshoe effect from multiple dimensionality reduction techniques applied to simulations, soil samples, and samples from postmortem mice. An in-depth understanding of this phenomenon allows targeting of niche differentiation patterns from high-level ordination plots, which can guide conventional statistical tools to pinpoint microbial niches along environmental gradients.

IMPORTANCE The horseshoe effect is often considered an artifact of dimensionality reduction. We show that this is not true in the case for microbiome data and that, in fact, horseshoes can help analysts discover microbial niches across environments.