A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy.

PMC3794901An algorithm is presented that returns the optimal pairwise gapped alignment of two sets of signed numerical sequence values. One distinguishing feature of this algorithm is a flexible comparison engine (based on both relative shape and absolute similarity measures) that does not rely on explicit gap penalties. Additionally, an empirical probability model is developed to estimate the significance of the returned alignment with respect to randomized data. The algorithm's utility for biological hypothesis formulation is demonstrated with test cases including database search and pairwise alignment of protein hydropathy. However, the algorithm and probability model could possibly be extended to accommodate other diverse types of protein or nucleic acid data, including positional thermodynamic stability and mRNA translation efficiency. The algorithm requires only numerical values as input and will readily compare data other than protein hydropathy. The tool is therefore expected to complement, rather than replace, existing sequence and structure based tools and may inform medical discovery, as exemplified by proposed similarity between a chlamydial ORFan protein and bacterial colicin pore-forming domain. The source code, documentation, and a basic web-server application are available.JH Libraries Open Access Fun

Association of Spinal Alignment Correction With Patient-Reported Outcomes in Adult Cervical Deformity: Review of the Literature

Objective Adult cervical deformity (ACD) is a debilitating spinal condition that causes significant pain, neurologic dysfunction, and functional impairment. Surgery is often performed to correct cervical alignment, but the optimal amount of correction required to improve patient-reported outcomes (PROs) are not yet well-defined. Methods A review of the literature was performed and Fisher z-transformation (Zr) was used to pool the correlation coefficients between alignment parameters and PROs. The strength of correlation was defined according to the following: poor (0 <r ≤ 0.3), fair (0.3 < r ≤ 0.5), moderate (0.5 < r ≤ 0.8), and strong (0.8 < r ≤1). Results Increased C2–7 sagittal vertical axis was fairly associated with increased Neck Disability Index (NDI) (pooled Zr=0.31; 95% confidence interval [CI], -0.03 to 0.58). Changes in T1 slope minus cervical lordosis poorly correlated with NDI (pooled Zr=-0.04; 95% CI, -0.23 to 0.30). Increased C7–S1 was poorly associated with worse EuroQoL 5-Dimension (pooled Zr=-0.22; 95% CI, -0.36 to -0.06). Correction of horizontal gaze did not correlate with legacy metrics. Modified Japanese Orthopedic Association correlated with C2-slope, C7–S1, and C2–S1. Conclusion Spinal alignment parameters variably correlated with improved health-related quality of life and myelopathy after corrective surgery for ACD. Further studies evaluating legacy PROs, Patient-Reported Outcomes Measurement System, and ACD specific instruments are needed for further validation

Dynamic Changes in Arteriovenous Malformations (AVMs): Spontaneous Growth and Resolution of AVM-Associated Aneurysms in Two Pediatric Patients

Arteriovenous malformations (AVMs) of the central nervous system are dynamic lesions that can change with time. One of the most clinically important concerns is the development and potential rupture of AVM-associated aneurysms. In this report, we review pediatric cases of de novo development of AVM-associated aneurysms in 2 children and present the relevant clinical and radiographic records. These 2 cases, coupled with a review of the current literature, offer insight into the risks of AVMs in children and underline the importance of timely treatment of appropriate cases