Stabilizing the Code—Methods to Preserve RNA Prove Their Worth

Commercially available platforms to stabilize messenger RNA (mRNA) and microRNA are critically designed to optimize and ensure the quality and integrity of those nucleic acids. This is not only essential for gene expression analyses, but would provide technical utility in providing concordant standard operating procedures in preserving the structural integrity of RNA species in multicenter clinical research programs and biobanking of cells or tissues for subsequent isolation of intact RNA. The major challenge is that the presence of degraded samples may adversely influence the interpretation of expression levels on isolated mRNA or microRNA samples and that in the absence of a concordant operating procedure between multiple collaborating research centers would confound data analysis and interpretation. However, in this issue of Biomarker Insights, Weber et al provide a detailed and critical analysis of two common RNA preservation systems, PAXgene and RNAlater. Such studies are lacking in the literature. However, the authors provide compelling evidence that not all conservation platforms are created equal and only one system proves its worth

Analytical and experimental investigation of mistuning in propfan flutter

An analytical and experimental investigation of the effects of mistuning on propfan subsonic flutter was performed. The analytical model is based on the normal modes of a rotating composite blade and a three-dimensinal subsonic unsteady lifting surface aerodynamic theory. Theoretical and experimental results are compared for selected cases at different blade pitch angles, rotational speeds, and free-stream Mach numbers. The comparison shows a reasonably good agreement between theory and experiment. Both theory and experiment showed that combined mode shape, frequency, and aerodynamic mistuning can have a beneficial or adverse effect on blade damping depending on Mach number. Additional parametric results showed that alternative blade frequency mistuning does not have enough potential for it to be used as a passive flutter control in propfans similar to the one studied. It can be inferred from the results that a laminated composite propfan blade can be tailored to optimize its flutter speed by selecting the proper ply angles

Tissue specific induction of p62/sqstm1 by farnesoid X receptor

Background: Farnesoid X Receptor (FXR) is a member of the nuclear receptor superfamily and is a ligand-activated transcription factor essential for maintaining liver and intestinal homeostasis. FXR is protective against carcinogenesis and inflammation in liver and intestine as demonstrated by the development of inflammation and tumors in the liver and intestine of FXR knock-out mice. However, mechanisms for the protective effects of FXR are not completely understood. This study reports a novel role of FXR in regulating expression of Sqstm1, which encodes for p62 protein. p62 plays an important role in maintaining cellular homeostasis through selective autophagy and activating signal transduction pathways, such as NF-κB to support cell survival and caspase-8 to initiate apoptosis. FXR regulation of Sqstm1 may serve as a protective mechanism. Methods and Results: This study showed that FXR bound to the Sqstm1 gene in both mouse livers and ileums as determined by chromatin immunoprecipitation. In addition, FXR activation enhanced transcriptional activation of Sqstm1 in vitro. However, wild-type mice treated with GW4064, a synthetic FXR ligand, showed that FXR activation induced mRNA and protein expression of Sqstm1/p62 in ileum, but not in liver. Interestingly, FXR-transgenic mice showed induced mRNA expression of Sqstm1 in both liver and ileum compared to wild-type mice. Conclusions: Our current study has identified a novel role of FXR in regulating the expression of p62, a key factor in protein degradation and cell signaling. Regulation of p62 by FXR indicates tissue-specific and gene-dosage effects. Furthermore, FXR-mediated induction of p62 may implicate a protective mechanism of FXR. © 2012 Williams et al

Engineering, Life Sciences, and Health/Medicine Synergy in Aerospace Human Systems Integration: The Rosetta Stone Project

In the realm of aerospace engineering and the physical sciences, we have developed laws of physics based on empirical and research evidence that reliably guide design, research, and development efforts. For instance, an engineer designs a system based on data and experience that can be consistently and repeatedly verified. This reproducibility depends on the consistency and dependability of the materials on which the engineer works and is subject to physics, geometry and convention. In life sciences and medicine, these apply as well, but individuality introduces a host of variables into the mix, resulting in characteristics and outcomes that can be quite broad within a population of individuals. This individuality ranges from differences at the genetic and cellular level to differences in an individuals personality and abilities due to sex and gender, environment, education, etc

Targeting lymphatic vessel functions through tyrosine kinases

The lymphatic vascular system is actively involved in tissue fluid homeostasis, immune surveillance and fatty acid transport. Pathological conditions can arise from injury to the lymphatics, or they can be recruited in the context of cancer to facilitate metastasis. Protein tyrosine kinases are central players in signal transduction networks and regulation of cell behavior. In the lymphatic endothelium, tyrosine kinases are involved in processes such as the maintenance of existing lymphatic vessels, growth and maturation of new vessels and modulation of their identity and function. As such, they are attractive targets for both existing inhibitors and the development of new inhibitors which affect lymphangiogenesis in pathological states such as cancer. RNAi screening provides an opportunity to identify the functional role of tyrosine kinases in the lymphatics. This review will discuss the role of tyrosine kinases in lymphatic biology and the potential use of inhibitors for anti-lymphangiogenic therapy

Comparing penalization methods for linear models on large observational health data

Objective: This study evaluates regularization variants in logistic regression (L1, L2, ElasticNet, Adaptive L1, Adaptive ElasticNet, Broken adaptive ridge [BAR], and Iterative hard thresholding [IHT]) for discrimination and calibration performance, focusing on both internal and external validation. Materials and Methods: We use data from 5 US claims and electronic health record databases and develop models for various outcomes in a major depressive disorder patient population. We externally validate all models in the other databases. We use a train-test split of 75%/25% and evaluate performance with discrimination and calibration. Statistical analysis for difference in performance uses Friedman's test and critical difference diagrams. Results: Of the 840 models we develop, L1 and ElasticNet emerge as superior in both internal and external discrimination, with a notable AUC difference. BAR and IHT show the best internal calibration, without a clear external calibration leader. ElasticNet typically has larger model sizes than L1. Methods like IHT and BAR, while slightly less discriminative, significantly reduce model complexity. Conclusion:L1 and ElasticNet offer the best discriminative performance in logistic regression for healthcare predictions, maintaining robustness across validations. For simpler, more interpretable models, L0-based methods (IHT and BAR) are advantageous, providing greater parsimony and calibration with fewer features. This study aids in selecting suitable regularization techniques for healthcare prediction models, balancing performance, complexity, and interpretability.</p

Practice in Child Phonological Disorders: Tackling some Common Clinical Problems

Goal of presentation is to identify areas of child phonology that clinicans have difficulty with

Novel wafer-scale adhesive bonding with improved alignment accuracy and bond uniformity

We report a versatile method for improving post-bonding wafer alignment accuracy and BCB thickness uniformity in stacks bonded with soft-baked BCB. It is based on novel BCB-based micro-pillars that act as anchors during bonding. The anchor structures become a natural part of the bonding interface therefore causing minimal interference to the optical, electrical and mechanical properties of the bonded stack. We studied these properties for fixed anchor density and various anchor heights with respect to the adhesive BCB thickness. We demonstrated that the alignment accuracy can be improved by approximately an order of magnitude and approach the fundamental pre-bond alignment accuracy by the tool. We also demonstrated that this technique is effective for a large range of BCB thicknesses of 2–16 μm. Furthermore we observed that the thickness non-uniformities were reduced by a factor of 2–3 × for BCB thicknesses in the 8–16 μm range

TLR2 and TLR4 as Potential Biomarkers of Environmental Particulate Matter Exposed Human Myeloid Dendritic Cells

In many subjects who are genetically susceptible to asthma, exposure to environmental stimuli may exacerbate their condition. However, it is unknown how the expression and function of a family of pattern-recognition receptors called toll-like receptors (TLR) are affected by exposure to particulate pollution. TLRs serve a critical function in alerting the immune system of tissue damage or infection—the so-called “danger signals”. We are interested in the role that TLRs play in directing appropriate responses by innate immunity, particularly dendritic cells (DC), after exposing them to particulate pollution. Dendritic cells serve a pivotal role in directing host immunity. Thus, we hypothesized that alterations in TLR expression could be further explored as potential biomarkers of effect related to DC exposure to particulate pollution. We show some preliminary data that indicates that inhaled particulate pollution acts directly on DC by down-regulating TLR expression and altering the activation state of DC. While further studies are warranted, we suggest that alterations in TLR2 and TLR4 expression should be explored as potential biomarkers of DC exposure to environmental particulate pollution

Differential receptor binding and regulatory mechanisms for the lymphangiogenic growth factors VEGF-C and VEGF-D

VEGF-C and VEGF-D are secreted glycoproteins that induce angiogenesis and lymphangiogenesis in cancer, thereby promoting tumor growth and spread. They exhibit structural homology and activate VEGFR-2 and VEGFR-3, receptors on endothelial cells that signal for growth of blood vessels and lymphatics. VEGF-C and VEGF-D were thought to exhibit similar bioactivities, yet recent studies indicated distinct signaling mechanisms (e.g. tumor-derived VEGF-C promoted expression of the prostaglandin biosynthetic enzyme COX-2 in lymphatics, a response thought to facilitate metastasis via the lymphatic vasculature, whereas VEGF-D did not). Here we explore the basis of the distinct bioactivities of VEGF-D using a neutralizing antibody, peptide mapping, and mutagenesis to demonstrate that the N-terminal α-helix of mature VEGF-D (Phe(93)–Arg(108)) is critical for binding VEGFR-2 and VEGFR-3. Importantly, the N-terminal part of this α-helix, from Phe(93) to Thr(98), is required for binding VEGFR-3 but not VEGFR-2. Surprisingly, the corresponding part of the α-helix in mature VEGF-C did not influence binding to either VEGFR-2 or VEGFR-3, indicating distinct determinants of receptor binding by these growth factors. A variant of mature VEGF-D harboring a mutation in the N-terminal α-helix, D103A, exhibited enhanced potency for activating VEGFR-3, was able to promote increased COX-2 mRNA levels in lymphatic endothelial cells, and had enhanced capacity to induce lymphatic sprouting in vivo. This mutant may be useful for developing protein-based therapeutics to drive lymphangiogenesis in clinical settings, such as lymphedema. Our studies shed light on the VEGF-D structure/function relationship and provide a basis for understanding functional differences compared with VEGF-C