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Metabolic pathways provide key information for achieving a better understanding of life and all its processes; this is useful information for the improvement of medicine, agronomy, pharmacy, and other similar areas. The main analysis tool used to study these pathways is based on pathway comparison, using graph data structures. Metabolic pathway comparison has been defined as a computationally complex task. In a previous work, two new algorithms were introduced to treat the problem of metabolic pathway pairwise comparison. Here we provide an extended analysis with more data and a deeper analysis of metabolic pathway comparison as listed in the discussion and results section.

Background Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. Results A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar’s ‘striped’ approach. Rognes’s SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail’s prefix scan implementation is generally the fastest, faster even than Farrar’s ‘striped’ approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Conclusions Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

PurposeIn response to sagittal malalignment, compensatory spinal and lower extremity mechanisms are recruited. Thoracolumbar realignment surgery has been shown to yield reciprocal changes in these compensations. Thus, whole-body radiographic assessment has come to the fore. This study aimed to evaluate the relationship between spinopelvic parameters and lower extremity compensation angles and to examine their coupled change with deformity correction.MethodsThis was a multicenter retrospective analysis of patients who had ≥ 4 levels posterior fusion, whole-body radiographs, and ≥ 2 years follow-up. Relative Pelvic Version (RPV), Relative Lumbar Lordosis (RLL), Relative Spinopelvic Alignment (RSA), Femoral Obliquity Angle (FOA), Knee Flexion Angle (KFA) and Global Sagittal Axis (GSA) were measured preoperatively and 6 week postoperatively. Kruskal–Wallis tests were performed to assess the relation of relative spinopelvic parameters to global sagittal alignment and lower extremity compensation angles. Spearman’s correlations were performed to assess correlations of pre-to-postoperative changes.Results193 patients (156F, 37 M) were included. The mean age was 57.2 ± 16.6 years. The mean follow-up duration was 50.6 (24–90) months. On average, 10.3 ± 3.8 levels were fused. Among the cohort, 124 (64.2%) had a sacral or sacroiliac fixation, and 43 (22.3%) had 3-column osteotomies. Preoperative FOA, KFA and GSA significantly differed between RPV, RLL and RSA categories. Significant weak-to-strong correlations were observed between spinopelvic parameters, global sagittal alignment and lower extremity compensation angles (rho range: − 0.351 to 0.767).ConclusionsPI-adjusted relative spinopelvic parameters significantly correlated with measurements of the lower extremity compensation. Postoperative changes in RPV, RLL and RSA reflected changes in FOA, KFA and GSA. These measurements may serve as a valuable proxy for surgical planning when whole-body imaging is not available.

Background There is a need for computational approaches to compare small organic molecules based on chemical similarity or for evaluating biochemical transformations. No tool currently exists to generate global molecular alignments for small organic molecules. The study introduces a new approach to molecular alignment in the Simplified Molecular Input Line Entry System (SMILES) format. This method leverages programming and scoring alignments to minimize differences in electronegativity, here using a measure of atomic partial charges to address the challenge of understanding structural transformations in reaction pathways. This can be applied to study transitions from linear to cyclical pathways. Results The proposed method is based on the Needleman-Wunsch algorithm for sequence alignment, but it uses a modified scoring function for different input data. Validation against a benchmarked dataset from the Krebs cycle, based on the known chemical transformations in the pathway, confirmed the efficacy of the approach in aligning atoms that are known to be the same across the transformation. The algorithm also quantified each transformation of metabolites in the Pentose Phosphate Pathway and in Glycolysis. The method was used to study the difference in chemical similarity over transformations between linear and cyclical pathways. The study found a midpoint dissimilarity peak in cyclical pathways (particularly the Krebs Cycle) and a progressive decrease in molecular similarity in linear pathways, consistent with expectations. Conclusions The study introduces an algorithm that quantifies molecular transformations in metabolic pathways. The algorithm effectively highlights structural changes and was applied to a hypothesis about the transition from linear to cyclical structures. The software, which provides valuable insights into molecular transformations, is available at: https://github.com/24atang/SMILES-Alignment.git

PurposeThis study aimed to validate the usefulness of the global alignment proportion (GAP) score to predict postoperative mechanical failure in the elderly (mean age, 70.5 years) individuals with severe sagittal imbalance.MethodsA total of 84 patients were enrolled: mechanical complications (MC), minor mechanical complications (mMC), proximal junctional failure (PJF), and revision surgery occurred in 61% (51/84), 58% (49/84), 44% (37/84), and 13% (11/84) of the patients, respectively. The GAP score was calculated using the X-ray obtained in the early postoperative period. The validity of the GAP score’s predictive ability was evaluated by calculating the area under the curve (AUC) of the receiver operating characteristics curve. Univariate logistic regression analysis and Cochran–Armitage test of trend were performed to determine the association between mechanical complications and GAP score.ResultsThe discriminatory power of GAP score to predict MC, mMC, and PJF was “moderately accurate,” with an AUC of 0.839 (confidence interval [CI] 0.755–0.824, p < 0.001), 0.836 (CI 0.749–0.923, p < 0.001), and 0.702 (CI 0.588–0.851, p < 0.001), respectively. The GAP score showed a statistically significant association with MC, mMC, and PJF in univariate logistic regression analysis and Cochran–Armitage test for trend. However, it was not significantly associated with revision surgery.ConclusionThis study showed promising results regarding the GAP score’s predictive power for MC, mMC, and PJF in the elderly population with degenerative kyphoscoliosis. Using the GAP score, we can determine the patient’s specific correction goal preoperatively to prevent mechanical failure based on individual patient’s characteristics such as pelvic incidence.

Purpose To investigate the impact of the Global Alignment and Proportion (GAP) score components on patient outcomes in Adult Spine Deformity (ASD) surgery. Methods Patients included underwent assessment via the GAP score and its individual components: pelvic version (GAP PV), lumbar lordosis (GAP LL), lumbar distribution index (GAP LDI) and spinopelvic component (GAP SP). Multivariable analyses assessed the association between alignment in these components and clinical outcomes in ASD patients. Results 762 ASD patients met inclusion criteria. Alignment in GAP SP independently predicted meeting MCID for SR-22S and ODI and was associated with a lower likelihood of developing mechanical complications. Patients aligned in GAP SP were less likely to develop proximal junctional kyphosis (OR 0.42, 0.26–0.73, p  = 0.01) and PJF (OR 0.3, 0.13–0.74, p  = 0.01). Proportioned alignment in GAP SP with disproportioned alignment in GAP LDI contributed to an increased risk of PJK and PJF (OR 2.67, 95% CI 1.95–6.82, p  = 0.045). There was no significant association of GAP SP proportionality and GAP RPV (OR 1.1, 0.86–2.15, p  = 0.253) or GAP LL (OR 1.34, 0.78–4.23, p  = 0.673) disproportionality with outcomes. Disproportioned alignment in GAP SP but proportioned alignment in both GAP LL and GAP LDI was associated with decreased likelihood of PJK (OR 0.53, 95% CI 0.39–0.94, p  = 0.02) and PJF (OR 0.31, 95% CI 0.19–0.67, p  = 0.001). Conclusion The spinopelvic component of the GAP score is the most significant independent predictor of clinical outcomes. Its interaction with the other components of the GAP score also aids assessment of the risk for mechanical complications.

PurposeThe purpose of this study was to determine the discriminatory ability of age-adjusted alignment offset and the global alignment and proportion (GAP) score parameters to predict postoperative mechanical complications.MethodsSurgical patients from the Adult Symptomatic Lumbar Scoliosis cohort were reviewed at 2 year follow up. Age-adjusted alignment offsets and GAP parameters were calculated for each patient. A series of nonlinear logistic regression models were fit, and the odds of mechanical complications were calculated. The discriminatory ability of the GAP score, GAP score parameters, and age-adjusted alignment offsets were determined plotting receiver operative characteristic (ROC) with the C statistic (AUC).ResultsA total of 165 patients were included. A total of 49 mechanical complications occurred in 41 patients (21 proximal junctional kyphosis and 28 pseudoarthrosis). The GAP score had no discriminatory ability in this cohort. Relative lumbar lordosis 15 degrees greater than ideal lumbar lordosis was associated with greater mechanical complications. A lumbar distribution index of 90% was associated with fewer mechanical complications compared to a lumbar distribution index of 65%. Age-adjusted offset alignment targets had no discriminatory ability to predict mechanical complications.ConclusionRadiographic alignment targets using either age-adjusted alignment target offset or GAP score parameters had minimal ability to predict mechanical complications in isolation. Mechanical complications following adult spinal deformity surgery are complex, and patient factors play a critical role.Clinical trial registeration This study was registered at ClinicalTrials.gov (number NCT00854828) in March 2009.

PurposeTo evaluate the association between global spinal malalignment and rapid progression of hip arthrosis.MethodsThis was a retrospective, case–control study including 90 patients, contributing 90 hips, who underwent hemi- or total hip arthroplasty at our institution. For analysis, hips were classified into a rapid progression group, defined as ≥ 2 mm destruction of the femoral head or loss of the hip joint space within a 12-month period (n = 30), and a non-rapid progression group, defined by no observable hip disease progression over a period more than 12 months (n = 60). Logistic regression analysis identified factors that predicted rapid progression, with a receiver operating characteristic curve analysis used to confirm factors.ResultsSignificant between-group differences were identified for the following parameters: pelvic tilt (P = 0.002, PT), sagittal vertical axis (P = 0.002, SVA), and T1 pelvic angle (P < 0.001, TPA). On multiple logistic regression, PT (P = 0.002), SVA (P = 0.002), and TPA (P < 0.001) were predictive of a rapid progression on hip arthrosis, with the area under the curve being greater for TPA than PT (P = 0.035).ConclusionGlobal spinal alignment is associated with rapid progression of hip arthrosis. TPA could assist in identifying patients at risk for rapid progression of hip arthrosis, allowing for time management.

The limited field of view of high-resolution microscopic images hinders the study of biological samples in a single shot. Stitching of microscope images (tiles) captured by the whole-slide imaging (WSI) technique solves this problem. However, stitching is challenging due to the repetitive textures of tissues, the non-informative background part of the slide, and the large number of tiles that impact performance and computational time. To address these challenges, we proposed the Fast and Robust Microscopic Image Stitching (FRMIS) algorithm, which relies on pairwise and global alignment. The speeded up robust features (SURF) were extracted and matched within a small part of the overlapping region to compute the transformation and align two neighboring tiles. In cases where the transformation could not be computed due to an insufficient number of matched features, features were extracted from the entire overlapping region. This enhances the efficiency of the algorithm since most of the computational load is related to pairwise registration and reduces misalignment that may occur by matching duplicated features in tiles with repetitive textures. Then, global alignment was achieved by constructing a weighted graph where the weight of each edge is determined by the normalized inverse of the number of matched features between two tiles. FRMIS has been evaluated on experimental and synthetic datasets from different modalities with different numbers of tiles and overlaps, demonstrating faster stitching time compared to existing algorithms such as the Microscopy Image Stitching Tool (MIST) toolbox. FRMIS outperforms MIST by 481% for bright-field, 259% for phase-contrast, and 282% for fluorescence modalities, while also being robust to uneven illumination.

PurposeTo evaluate the association between the preoperative global alignment and proportion (GAP) score and low back pain (LBP) after total hip arthroplasty (THA).MethodsThis was a retrospective case–control study of 200 patients who underwent primary unilateral THA for hip osteoarthritis. The following variables were compared between individuals with (n = 76) and without (n = 124) LBP after THA over a mean follow-up of 2 years: age, sex, GAP score, and patient-reported outcome measures. Logistic regression and receiver operating characteristic curve analyses were used to detect predictive factors.ResultsThe following parameters were predictive of post-THA LBP: relative pelvic version (RPV) <−7° (odds ratio, 1.43; 95% confidence interval, 1.10–1.72; P = 0.032) and relative lumbar lordosis <−15° (odds ratio, 1.13; 95% confidence interval, 1.04–2.13; P = 0.041) preoperatively. Using an RPV cutoff value of − 7° (specificity 61/64 = 0.953; sensitivity 121/136 = 0.890), there were significant between-group differences in LBP visual analog scale (P = 0.020), Oswestry Disability Index (ODI, P = 0.014), EuroQol 5-Dimension (P = 0.027), Hip Disability and Osteoarthritis Outcome Score Joint Replacement (HOOS JR, P = 0.012), patient satisfaction (P = 0.024). There was clinically meaningful improvement for LBP visual analog scale (P = 0.001), ODI (P = 0.004), and HOOS JR (P < 0.001). The RPV before THA was correlated with HOOS JR (r = 0.773, P = 0.012) and ODI (r = − 0.602, P = 0.032) postoperatively.ConclusionAmong the GAP score, a moderate-to-severe pelvic retroversion was significantly associated with LBP post-THA. The RPV measurement may be a useful predictor of THA outcome, which may influence patient satisfaction.