Alignment Score Research Articles

Novel radiological predictors for the progression of proximal junctional kyphosis in osteoporotic vertebral compression fracture with kyphosis following posterior corrective surgery.

This study aimed to identify the effect of some novel risk factors associated with L1 vertebrae and parameters closely related to the sagittal alignment for the occurrence of proximal junctional kyphosis (PJK) following surgery for patients with osteoporotic vertebral compression fractures (OVCF)kyphosis. 74 OVCF patients undergoing posterior corrective surgery between January 2008 and June 2021 with a minimum 2-year follow-up were included. These patients were divided into PJK and non-PJK groups. Spinopelvic parameters, includingthoracolumbar slope (TLS)and the L1 plumb line (L1PL) were measured preoperatively, postoperatively, and at follow-up. Multivariate logistic analysis was performed on various risk factors and Global Alignment and Proportion (GAP) scores. Associations between novel parameters and PJK were analyzed using receiver operating characteristic(ROC) analysis. PJK was identified in 28.4% of patients. The mean age and follow-up were 63.45years and 38.17months, respectively. There was no difference between the PJK and the non-PJK groups in baseline demographics, pre-operative and immediate post-operative pelvic incidence-lumbar lordosis mismatch. Multiple comparisonsshowed that the proportion of PJK in the severely disproportioned group(the group with the highest GAP scores) and that of the other two groups with lower GAP scores were statistically different (P < 0.001). Potential risk factors for PJK included preoperative thoracic kyphosis (TK) (P < 0.001), TLS (P = 0.016), postoperative TLS (P < 0.001), and L1PL (P < 0.001). Postoperative TLS and L1PL were respectively independent risk factors for PJK, with the cut-off values set at 8.6° and 10.4mm to predict the occurrence of PJK. TLS and L1PL can be used to predict the occurrence of PJK in patients undergoing surgery for OVCF and are crucial for preventing the progression of PJK. Achieving a proportionate GAP Score postoperatively seems to be a viable option as higher GAP scores were associated with higher rates of PJK.

ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring.

Efficient virtual screening techniques are critical in drug discovery for identifying potential drug candidates. We present an open-source package for molecular alignment and 3D similarity calculations optimized for large-scale virtual screening of small molecules. This work parallels widely used proprietary tools and offers an approach complementary to structure-based virtual screening. Our package employs the PAPER software for optimizing molecular alignments based on Gaussian volume overlaps. GPU acceleration is utilized to significantly reduce computational time and resource requirements. After obtaining the optimal alignments between the target and the query molecules, both shape and color (based on pharmacophore features) scores are computed to assess molecular similarity, with aligned molecules optionally being output in sdf format. The package was benchmarked using the DUDE-Z public data sets. Results demonstrated the package's near-state-of-the-art performance and robustness across multiple target classes, with speed that enables many routine ligand-based drug discovery workflows. As an open-source and freely available resource (github.com/molecularinformatics/roshambo) with both a convenient Python API and command line interface, our package also addresses the need for accessible and efficient virtual screening tools in drug discovery.

Course-Skill Atlas: A national longitudinal dataset of skills taught in U.S. higher education curricula

Higher education plays a critical role in driving an innovative economy by equipping students with knowledge and skills demanded by the workforce. While researchers and practitioners have developed data systems to track detailed occupational skills, such as those established by the U.S. Department of Labor (DOL), much less effort has been made to document which of these skills are being developed in higher education at a similar granularity. Here, we fill this gap by presenting Course-Skill Atlas – a longitudinal dataset of skills inferred from over three million course syllabi taught at nearly three thousand U.S. higher education institutions. To construct Course-Skill Atlas, we apply natural language processing to quantify the alignment between course syllabi and detailed workplace activities (DWAs) used by the DOL to describe occupations. We then aggregate these alignment scores to create skill profiles for institutions and academic majors. Our dataset offers a large-scale representation of college education’s role in preparing students for the labor market. Overall, Course-Skill Atlas can enable new research on the source of skills in the context of workforce development and provide actionable insights for shaping the future of higher education to meet evolving labor demands, especially in the face of new technologies.

Formal wellness training of academic radiology leaders improves work-life conflict.

To investigate the effect of formal leadership training of academic radiology leaders within an academic center on their own burnout and professional fulfillment. The study cohort was academic radiology leaders within one of the largest academic organizations of academic radiologists within the United States. All academic radiology leaders within the organization were electronically mailed a weblink to a confidential IRB-approved survey in April 2021. The survey included validated questions from the Stanford Professional Fulfillment Index (PFI), values alignment, teamwork, overload, and work-family conflict. Academic leaders were invited in May 2021 to participate in instructor-led formal training on leading wellness focusing on 5 core leadership skills - emotional intelligence, self-care, resilience support, demonstrating care, and managing burnout. An identical follow-up survey was electronically mailed 6 months after initial training in November 2021. The overall response rate of academic radiology leaders was 59% (19/32). For both measures, there was acceptable internal consistency (Cronbach's α = 0.63 for work exhaustion and α = 0.90 for fulfillment). There was a statistically significant improvement in work-family conflict (3.32 vs 2.86; p = 0.04). No statistically significant differences were identified for fulfillment, work exhaustion, alignment, work overload, and teamwork scores after training. Formal instruction in leading wellness improved work-life conflict for academic radiology leaders. There was no significant change in burnout, fulfillment nor organizational alignment of the leaders. Formal instruction in leading wellness raised awareness and improved work-life conflict in academic radiology leaders.

Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain

AbstractMany polymerases and other proteins are endowed with a catalytic domain belonging to the nucleotidyltransferase fold, which has also been deemed the non-canonical palm domain, in which three conserved acidic residues coordinate two divalent metal ions. Tertiary structure-based evolutionary analyses provide valuable information when the phylogenetic signal contained in the primary structure is blurry or has been lost, as is the case with these proteins. Pairwise structural comparisons of proteins with a nucleotidyltransferase fold were performed in the PDBefold web server: the RMSD, the number of superimposed residues, and the Qscore were obtained. The structural alignment score (RMSD × 100/number of superimposed residues) and the 1-Qscore were calculated, and distance matrices were constructed, from which a dendogram and a phylogenetic network were drawn for each score. The dendograms and the phylogenetic networks display well-defined clades, reflecting high levels of structural conservation within each clade, not mirrored by primary sequence. The conserved structural core between all these proteins consists of the catalytic nucleotidyltransferase fold, which is surrounded by different functional domains. Hence, many of the clades include proteins that bind different substrates or partake in non-related functions. Enzymes endowed with a nucleotidyltransferase fold are present in all domains of life, and participate in essential cellular and viral functions, which suggests that this domain is very ancient. Despite the loss of evolutionary traces in their primary structure, tertiary structure-based analyses allow us to delve into the evolution and functional diversification of the NT fold.

Predicting postoperative mechanical complications with the ethnicity-adjusted global alignment and proportion score in degenerative scoliosis: does paraspinal muscle degeneration matter?

The global alignment and proportion (GAP) score was developed to predict mechanical complications (MCs) after adult spinal deformity surgery but showed limited sensitivity in the Asian population. Considering variations in sagittal parameters among different ethnic groups, our team developed the ethnicity-adjusted GAP score according to the spinopelvic parameters of 566 asymptomatic Chinese volunteers (C-GAP score). Notably, degenerative scoliosis (DS) patients with MCs following corrective surgery have more severe paraspinal muscle degeneration. For DS patients with various sagittal alignments, the unevenly distributed degeneration of paraspinal muscle may exert different influences on MC occurrence and largely affect the accuracy of the C-GAP score in clinical assessment. Therefore, incorporating paraspinal muscle degeneration indices within the C-GAP score may improve its accuracy in predicting MC occurrence. We aimed to clarify the influence of paraspinal muscle degeneration on the C-GAP score predicting MC occurrence following DS surgery and modify the C-GAP score with paraspinal muscle degeneration parameters. A retrospective case-control study. 107 adult degenerative scoliosis patients. Demographic information, postoperative sagittal spinopelvic parameters, the GAP score, the C-GAP score, and paraspinal muscle degeneration parameters. A total of 107 DS patients undergoing posterior spinal fusion surgery (≥4 vertebrae) with a minimum of 2 years follow-up (or experiencing MCs within 2 years) were retrospectively reviewed. Their C-GAP score was calculated based on our previous study and patients were divided into 3 C-GAP categories, "proportioned" (P), "moderately disproportioned" (MD), and "severely disproportioned" (SD). Relative cross-sectional area (cross-sectional area of muscle-disc ratio×100, rCSA) and fat infiltration rate, FI% at L1/2, L2/3, L3/4, and L4/5 discs were quantitatively evaluated using magnetic resonance imaging (MRI). In each C-GAP category, patients were additionally divided into the MC group and the non-MC group to analyze their paraspinal muscle degeneration. A multivariable logistic regression model consisting of the CSA-weighted average FI% (total FI%) and the C-GAP score, C-GAPM was constructed. The area under the curve (AUC) of the receiver operating characteristic (ROC) curves was used to evaluate the predictability of the GAP score, the C-GAP score, FI%, and C-GAPM. This project was supported by the National Natural Science Foundation of China (No.82272545) and Special Fund of Science and Technology Plan of Jiangsu Province (No.BE2023658). For all 107 patients, FI% at L1/2, L2/3, L3/4, and L4/5 discs and the total FI% of the MC group (n=32) were significantly higher than those of the non-MC group (n=75). The MC rates of 3 original GAP categories, P, MD, and SD categories were 25.00% (6/24), 27.03%(10/37), and 34.78% (16/46) (χ2=0.944, p=0.624). Based on the C-GAP score, the MC rates of the P, MD, and SD categories were 11.90% (5/42), 34.69% (17/49), and 62.50% (10/16), showing significant differences (χ2=15.137, p=0.001). In the C-GAP MD category, compared with the non-MC group (n=32), the MC group (n=17) has a higher total FI% (26.16(22.95, 34.00) vs. 22.67(16.39, 27.37)), p=0.029). A similar trend was identified in the C-GAP SD category (34.79±11.56 vs. 19.00±5.17, p=0.007), but not in the C-GAP P category (25.09(22.82, 32.66) vs. 24.66(17.36, 28.63), p=0.361). The AUC of the GAP score, the C-GAP score, the total FI%, and C-GAPM were respectively 0.601, 0.722, 0.716, and 0.772. Paraspinal muscle degeneration exerts a significant effect on the occurrence of MC in the C-GAP MD, SD instead of P category. The integration of paraspinal muscle FI% with the C-GAP score (C-GAPM) enables a more accurate prediction of MCs following DS surgery. Surgeons should pay adequate attention to paraspinal muscle degeneration during surgical planning and postoperative management for patients in the C-GAP MD and SD categories.

Long term mechanical failure in well aligned adult spinal deformity patients

BACKGROUND CONTEXTMechanical complications (MC) are frequently linked to suboptimal postoperative alignment and represent a primary driver of revision surgery in the context of Adult Spinal Deformity (ASD). However, it's worth noting that even among those deemed "well aligned," the risk of experiencing MCs persists, hinting at the potential influence of factors beyond alignment. PURPOSEThe aim was to assess the incidence of MCs among well-aligned patients and delving into the relevant risk factors and surgical outcomes that come into play within this specific subgroup. STUDY DESIGN/SETTINGA retrospective analysis was conducted using data from a prospective multicenter database dedicated to ASD. PATIENT SAMPLEThe study focused on patients aged 55 years or older, who had a minimum follow-up period of 2 years, and exhibited a Global Alignment and Proportion (GAP) score of 2 points or less (excluding age) within 6 weeks of their index surgery. OUTCOME MEASURESMechanical complications such as rod fractures, pseudarthrosis, or junctional kyphosis or failure, METHODSPatients who developed mechanical complications were identified. Comparative analyses were performed, encompassing both continuous and categorical variables. Furthermore, binary logistic regression tests were employed to pinpoint risk factors, and ROC curves were used to determine the optimal threshold values for these variables. RESULTSA total of 83 patients met the inclusion criteria for this study, with a mean age of 66 years. On average, they had 10 instrumented levels, and 77% of them had fusion extending to the pelvis. Additionally, 27% of the patients had undergone 3-column osteotomies (3-CO). Among them, 33 patients (40%) experienced at least 1 MC during an average follow-up period of 4 years, which included 14 cases of proximal junctional kyphosis (PJK) and 20 cases of nonunion or rod breakage. 15 patients (18%) required revision surgery specifically for MC. In univariable analyses, patients who developed MC were characterized by higher body weight, poorer baseline general health (as indicated by worse SF-36 scores), and less favorable preoperative coronal and sagittal alignment. They also had longer hospital stays, a greater number of instrumented levels, and achieved less favorable postoperative coronal and sagittal alignment. Interestingly, factors such as 3-column osteotomies, postoperative bracing, and the addition of an anterior approach did not significantly alter the risk of MC in well-aligned adult spinal deformity (ASD) patients. Binary regression models revealed that independent risk factors for MC included the residual coronal lumbosacral curve, the number of instrumented levels, and Relative Spinopelvic Alignment (RSA). ROC curves identified an optimal threshold of a residual lumbosacral curve of ≤4° and RSA of ≤3°. Moreover, the rate of MCs showed a stepwise increase within the GAP-Proportioned group, with rates of 31% for GAP=0, 54% for GAP=1, and 75% for GAP=2, with RSA emerging as the most influential parameter. Lastly, patients with MC exhibited poorer functional and radiological outcomes at their last follow-up assessment. CONCLUSIONSThe rate of MCs remains elevated in sagittally “well-aligned” ASD patients that can be attributed to suboptimal residual sagittal and coronal malalignment, which in turn leads to poorer functional outcomes. This study reaffirms the multifaceted nature of MCs and underscores the significance of achieving impeccable postoperative alignment, particularly in the presence of additional risk factors such as extensive surgical correction, a high lever arm (involving instrumented vertebrae), excessive body weight, and frailty (as indicated by SF-36 scores).

Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner.

Recently developed long-read RNA sequencing technologies promise to provide a more accurate and comprehensive view of transcriptomes compared to short-read sequencers, primarily due to their capability to achieve full-length sequencing of transcripts. However, realizing this potential requires computational tools tailored to process long reads, which exhibit a higher error rate than short reads. Existing methods for assembling and quantifying long-read data often disagree on expressed transcripts and their abundance levels, leading researchers to lack confidence in the transcriptomes produced using this data. One approach to address the uncertainties in transcriptome assembly and quantification is by assigning the long reads to transcripts, enabling a more detailed characterization of transcript support at the read level. Here, we introduce TranSigner, a versatile tool that assigns long reads to any input transcriptome. TranSigner consists of three consecutive modules performing: read alignment to the given transcripts, computation of read-to-transcript compatibility based on alignment scores and positions, and execution of an expectation-maximization algorithm to probabilistically assign reads to transcripts and estimate transcript abundances. Using simulated data and experimental datasets from three well-studied organisms - Homo sapiens, Arabidopsis thaliana, and Mus musculus - we demonstrate that TranSigner achieves accurate read assignments, obtaining higher accuracy in transcript abundance estimation compared to existing tools.

Annotation Vocabulary (Might Be) All You Need.

Protein Language Models (pLMs) have revolutionized the computational modeling of protein systems, building numerical embeddings that are centered around structural features. To enhance the breadth of biochemically relevant properties available in protein embeddings, we engineered the Annotation Vocabulary, a transformer readable language of protein properties defined by structured ontologies. We trained Annotation Transformers (AT) from the ground up to recover masked protein property inputs without reference to amino acid sequences, building a new numerical feature space on protein descriptions alone. We leverage AT representations in various model architectures, for both protein representation and generation. To showcase the merit of Annotation Vocabulary integration, we performed 515 diverse downstream experiments. Using a novel loss function and only $3 in commercial compute, our premier representation model CAMP produces state-of-the-art embeddings for five out of 15 common datasets with competitive performance on the rest; highlighting the computational efficiency of latent space curation with Annotation Vocabulary. To standardize the comparison of de novo generated protein sequences, we suggest a new sequence alignment-based score that is more flexible and biologically relevant than traditional language modeling metrics. Our generative model, GSM, produces high alignment scores from annotation-only prompts with a BERT-like generation scheme. Of particular note, many GSM hallucinations return statistically significant BLAST hits, where enrichment analysis shows properties matching the annotation prompt - even when the ground truth has low sequence identity to the entire training set. Overall, the Annotation Vocabulary toolbox presents a promising pathway to replace traditional tokens with members of ontologies and knowledge graphs, enhancing transformer models in specific domains. The concise, accurate, and efficient descriptions of proteins by the Annotation Vocabulary offers a novel way to build numerical representations of proteins for protein annotation and design.

Does extreme weight loss after bariatric surgery alter spinopelvic parameters and ameliorate back pain? A retrospective case study.

The aim of this study was to evaluate the effect of extreme weight loss on low back pain and spinopelvic parameters. A total of 45 patients (11 males, 34 females; mean age: 40.2±9.4 years; range, 18 to 57 years) who had bariatric surgery between January 2018 and December 2021 were retrospectively analyzed. Radiological spinopelvic parameters including lumbar lordosis (LL), pelvic incidence (PI), spinopelvic harmony (when PI is within LL±10°), pelvic tilt (PT) and sacral slope (SS) were evaluated pre- and postoperatively. Clinical outcomes were assessed using the Visual Analog Scale-Back Pain (VAS-BP) and Oswestry Disability Index (ODI). The mean BMI loss at the end of the first year after surgery was 28.1±6.7% (range, 21 to 36%). The mean PI was 55.75°±12.47° preoperatively and 53.64°±11.86° at one year and the difference was -3.10°±5.25 (p=0.02), 1.10°±4.95° for PT (p=0.46), -2,70°±3.50° for SS (p<0.001), and 3.1±6.55 for LL (p<0.001). At one year, spinopelvic harmony remained unchanged in 31 patients, nine patients regained harmony, and was lost in five patients who had previously. No significant correlation between alterations in spinopelvic alignment and ODI scores was shown (p<0.05). The mean VAS-BP score was 40±30 mm preoperatively, and 20±3.5 mm postoperatively, indicating a difference of -39±29.5 (p<0.001). The mean ODI was 34.71±20.87 preoperatively, and 16±24 postoperatively, indicating a difference of -15±13 (p<0.001). Subgroup analyses showed that the change in SS was more pronounced with regard to PT change, particularly in young and female patients with >10 kg/m2 reduction in BMI (p<0.001). Weight loss after bariatric surgery improves lower back pain leading to changes in PT without affecting SS and altering PI.

Alignment assessment of anisotropic liquid crystals through an automated image processing algorithm

Liquid crystals (LCs) are recognised as an emerging type of responsive and functional materials that exhibit diverse technological applications. The spatial arrangement or alignment of LC molecules creates an optical anisotropy, which influences the propagation of light. This study presents an automated image processing algorithm designed to quantitatively assess LC alignment. The algorithm calculates the image structure tensor and computes a score ranging from 0 to 1 to represent the uniformity of LC alignment. The tool was verified on both artificially generated images of lines with pre-defined orientations and then tested on microscope images of LCs. For the latter, test samples of deformed helix ferroelectric LCs were constructed using three different alignment methods. Analysis of microscopic images of samples prepared utilising photoalignment, polymer rubbing, and oblique evaporation alignment techniques, determined average alignment scores (mean ± standard error of the mean) of 0.44 ± 0.03, 0.26 ± 0.1, and 0.17 ± 0.04, respectively, in comparison to commercially sourced control samples with a score of 0.64 ± 0.03 (n=5 each). This study paves the way for automated objective assessment of LC alignment, a critical aspect to ensure the optimal performance, reliability, and efficiency of various devices and sensors relying on LC technology.

Identification and impact of failure of pelvic compensation in patients with adult spinal deformity

BACKGROUND CONTEXTPrevious research has identified a specific subtype known as failure of pelvic compensation (FPC) in patients with adult spinal deformity (ASD). However, the criteria for assessing FPC remain inconsistent, and its impacts on spinal sagittal alignment and health-related quality-of-life (HRQoL) scores remain unclear. PURPOSETo propose a novel criterion for identifying FPC based on variations in spinopelvic alignment during the transition from the supine to upright position and to evaluate the effects of FPC on patients' spinal sagittal alignment and HRQoL scores. STUDY DESIGN/SETTINGRetrospective cross-sectional study. PATIENT SAMPLEPatients with ASD from a monocenter database. OUTCOME MEASURESRadiographic measures, including thoracic kyphosis (TK), lumbar lordosis (LL), sacral slope (SS), pelvic tilt, pelvic incidence (PI), and sagittal vertical axis (SVA), were measured on lateral whole-spine radiographs. LL and SS were also measured on reconstructed lumbar computed tomography images in the sagittal view taken in the supine position. The relative functional cross-sectional area (rFCSA) of paraspinal muscles was evaluated via lumbar magnetic resonance imaging. HRQoL measures, encompassing visual analog scale for back pain (VAS-BP), Oswestry Disability Index (ODI), and Scoliosis Research Society-22R (SRS-22R), were collected. METHODSA total of 154 patients were enrolled. Based on the calculated minimum detectable change of SS, FPC was defined as the change in SS of less than 3.4° between supine and upright positions. Patients were divided into 3 groups: sagittal balance with pelvic compensation (SI-PC), sagittal imbalance with pelvic compensation (SI-PC), and sagittal imbalance with failure of pelvic compensation (SI-FPC). Radiographic parameters and HRQoL scores were compared among the groups. RESULTSThirty-six patients were categorized into the SB-PC group, 87 into the SI-PC group, and 31 into the SI-FPC group. Patients with low PI and small paraspinal muscles rFCSA were more prone to experiencing FPC accompanied by severe sagittal imbalance. The SI-FPC group exhibited less TK and a larger SS than the SI-PC group exhibited and had a similar SVA as that of the SI-PC group. Additionally, they displayed worse VAS-BP, ODI, SRS-function, and SRS-22 total scores than the SB-PC group displayed. CONCLUSIONSIn patients with ASD, an inherently low pelvic compensatory reserve and a high fatty infiltration in paraspinal muscles are pivotal factors contributing to FPC. Compared with SI-PC patients, SI-FPC patients demonstrate a thoracic-dominant compensatory pattern for sagittal malalignment. In addition, these patients experienced more severe pain and functional decline than the SB-PC patients experienced.

ESKEMAP: exact sketch-based read mapping

BackgroundGiven a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a “similar sequence”. Traditionally, “similar sequence” was defined as having a high alignment score and read mappers were viewed as heuristic solutions to this well-defined problem. For sketch-based mappers, however, there has not been a problem formulation to capture what problem an exact sketch-based mapping algorithm should solve. Moreover, there is no sketch-based method that can find all possible mapping positions for a read above a certain score threshold.ResultsIn this paper, we formulate the problem of read mapping at the level of sequence sketches. We give an exact dynamic programming algorithm that finds all hits above a given similarity threshold. It runs in O(|t|+|p|+ℓ2)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O} (|t| + |p| + \\ell ^2)$$\\end{document} time and O(ℓlogℓ)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathcal {O} (\\ell \\log \\ell )$$\\end{document} space, where |t| is the number of k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document}-mers inside the sketch of the reference, |p| is the number of k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document}-mers inside the read’s sketch and ℓ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\ell$$\\end{document} is the number of times that k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document}-mers from the pattern sketch occur in the sketch of the text. We evaluate our algorithm’s performance in mapping long reads to the T2T assembly of human chromosome Y, where ampliconic regions make it desirable to find all good mapping positions. For an equivalent level of precision as minimap2, the recall of our algorithm is 0.88, compared to only 0.76 of minimap2.

Postural alignment is impaired in adults with severe mobility limitations after an acquired brain injury: an observational study

Background: Postural alignment impairments can be observed after acquired brain injury (ABI) and may be more prevalent in people with greater mobility impairment. However, investigations of postural alignment are limited by the lack of an evaluated method of assessment. This study examined postural alignment differences between healthy adults and adults with ABI, and evaluated repeatability of a new kinematic method for measuring postural alignment. Methods: Observational study of 14 adults with ABI who were non-ambulant at eight weeks post-injury, and 14 healthy adults. 3D kinematic data were recorded using motion capture technology in sitting and standing, on two separate days. A new Postural Alignment and Dispersion (PAD) score quantified average body segment displacements from the base of support (BoS) in the transverse plane. The two groups’ PAD scores were compared. Repeatability of the PAD score between days was evaluated using intraclass correlation coefficients (ICCs). Major findings: Greater postural alignment deviations were observed after ABI, including marked deficits in frontal and sagittal planes. ICCs ranged moderate (0.614) to excellent (0.945). Wide confidence intervals (CIs) for some ICCs indicated that repeatability of PAD scores could not be assured for all sitting and standing conditions. Conclusions: Postural alignment impairments occur in multiple planes after ABI and can be pronounced in people with severe mobility impairment. Evidence is needed to determine if addressing postural alignment impairments affects functional progress after ABI. PAD score measurement requires further evaluation to determine how repeatability can be optimised.

Preoperative low Hounsfield units in the lumbar spine are associated with postoperative mechanical complications in adult spinal deformity.

To determine the most valid bone health parameter to predict mechanical complications (MCs) following surgery for adult spinal deformity (ASD). This multicenter study retrospectively examined the records of patients who had undergone fusion of three or more motion segments, including the pelvis, with a minimum two-year follow-up period. Patients with moderate and severe global alignment and proportion scores were included in the study and divided into two groups: those who developed MCs and those who did not. Bone mineral density (BMD) of the lumbar spine and femoral neck was measured using dual-energy X-ray absorptiometry, and Hounsfield units (HUs) were measured in the lumbar spine on computed tomography. Radiographic parameters were evaluated preoperatively, immediately after surgery, and at final follow-up. Of 108 patients, 30 (27.8%) developed MCs, including 26 cases of proximal junctional kyphosis/failure, 2 of distal junctional failure, 6 of rod fracture, and 11 reoperations. HUs were significantly lower in patients who experienced MCs (113.7 ± 41.1) than in those who did not (137.0 ± 46.8; P = 0.02). BMD did not differ significantly between the two groups. The preoperative and two-year postoperative global tilt, as well as the immediately postoperative sagittal vertical axis, were significantly greater in patients who developed MCs than in those who did not (P = 0.02, P < 0.01, and P = 0.01, respectively). Patients who experienced MCs following surgery for ASD had lower HUs than those who did not. HUs may therefore be more useful than BMD for predicting MCs following surgery for ASD.

A Study on the Effects of Different Interaction Combinations and Language Levels on Continuous Writing in Online Environments

This study was conducted with non-English sophomore students, aiming to explore the effects of different interaction combinations and language levels on continuous writing in an online environment, and compare the differences in lexical alignments and composition quality of learners with different interaction combinations and language levels in the same continuous writing task through experiments. The results show that the mean values of the word-phrase alignment of the paired group were higher than those of the individual group in different interaction combinations, and the two groups showed significant differences; in terms of composition quality, the individual group was better than the paired group, but there was no significant difference between the two groups in terms of task continuation. Secondly, the word-phrase alignment and composition scores of the different language-level groups were higher than those of the same language-level groups, and there was a significant difference between the two groups in terms of word-phrase alignments, but not in terms of composition scores. The results of this study can be useful and informative for second language teachers in future continuous teaching in online environments.

Comparison of Global Alignment and Proportion (GAP) Score and SRS-Schwab ASD Classification in the Analysis of Surgical Outcomes for Adult Spinal Deformity

Study designThe GAP score predicted post-operative mechanical complications more effectively whereas SRS-Schwab classification improved evaluation of postoperative PROMs.ObjectiveThe study compared the GAP Score and SRS-Schwab Classification in predicting surgical outcomes for adult spinal deformity (ASD) and elucidated whether both systems should be included in the preoperative planning.Materials and methodsRadiographic measurements and health-related quality of life scores at baseline, 6 weeks after surgery, and the last follow-up were collected from a cohort of 69 ASD patients subjected to long segment spinal fusion surgery after they were grouped by GAP score and SRS-Schwab classification respectively. Fisher's exact test and receiver operator characteristic (ROC) curve analysis was used to compare the incidence of mechanical complications and the discriminant capacity during revision surgery between the two groups. Postoperative patient-reported outcomes measures (PROMs) were compared by one-way ANOVA, and the proportions of MCID achieved for PROMs compared by chi-square test between the two groups.ResultsThe overall incidence of mechanical complications and revision surgery were 42% and 8.7%. Both GAP score and its categories predicted mechanical complications and revision surgery, but the GAP score system could not predict the improvements of PROMs. The SRS-Schwab classification could predict the occurrence of postoperative mechanical complications and improvements of postoperative PROMs between the aligned, moderately misaligned and severely misaligned groups (P < 0.05).ConclusionHence, a comprehensive surgical strategy for postoperative planning may improve patients’ quality of life and minimize mechanical complications.Graphical

Effectiveness of vertical compression of locking plate combined with hollow screws in treatment of Sanders type Ⅱ and Ⅲ calcaneal fractures

To probe into the effectiveness of vertical compression of locking plate combined with hollow screws in the treatment of Sanders type Ⅱ and Ⅲ calcaneal fractures. The clinical data of 128 patients with Sanders type Ⅱ and Ⅲ calcaneal fractures who were admitted between March 2019 and April 2022 and met the selection criteria were retrospectively analyzed. Among them, 65 patients were treated with locking plate combined with hollow screw vertical compression (study group), and 63 patients were treated with simple locking plate (control group). There was no significant difference in baseline data between the two groups ( P>0.05), such as gender, age, fracture side and Sanders classification, cause of injury, time from injury to operation. The operation time, intraoperative blood loss, hospital stay, and fracture healing time were recorded and compared between the two groups. Before operation and at 12 months after operation, the American Orthopaedic Foot and Ankle Association (AOFAS) score (including total score, pain score, functional score, and alignment score) was used to evaluate the recovery of foot function, and imaging indicators such as calcaneal width, calcaneal height, calcaneal length, Böhler angle, and Gissane angle were measured on X-ray films. All patients were followed up 12 months after operation. There was no significant difference in operation time, intraoperative blood loss, hospital stay, and fracture healing time between the two groups ( P>0.05). Poor wound healing occurred in 1 case in the study group and 2 cases in the control group. At 12 months after operation, there was no significant difference between the two groups in the pre- and post-operative difference of calcaneal length, calcaneal height, Gissane angle, and Böhler angle ( P>0.05). However, the pre- and post-operative difference in calcaneal width in the study group was significantly higher than that in the control group ( P<0.05). The pre- and post-operative difference of AOFAS total score in the study group was significantly higher than that in the control group ( P<0.05), and further analysis showed that the pre- and post-operative difference of pain and function scores in the study group were significantly higher than those in the control group ( P<0.05), while there was no significant difference in the pre- and post-operative difference of force score between the two groups ( P>0.05). Compared with simple locking plate treatment, the treatment of Sanders type Ⅱ and Ⅲ calcaneal fractures with vertical compression of locking plate combined with hollow screws can more effectively improve the width of the subtalar calcaneal articular surface, avoid peroneal longus and brevis impingement, reduce pain, and increase the range of motion of the subtalar joint, and the effectiveness is better.

Assessing Strategic Business and IT Alignment: Validation of a Novel Model across Moroccan Enterprises

Strategic alignment between Business and IT remains a critical factor for organizational effectiveness, but measuring it often presents a complex challenge. This paper evaluates the model we proposed in previous work to measure the degree of alignment between Business strategy and IT initiatives. We applied the model to a selection of Moroccan companies. We compared the alignment scores obtained with those from the established Strategic Alignment Maturity Model (SAMM) using Cohen’s Kappa and simple linear regression for comparative analysis. This study demonstrates our model’s effectiveness in evaluating continuous scores and provides substantial concordance in categorical maturity assessments. Our validation confirms that our model can apply to various business contexts, paving the way for further refinement to evaluate business-IT alignment strategies.

TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments.

Accurate multiple sequence alignment (MSA) is imperative for the comprehensive analysis of biological sequences. However, a notable challenge arises as no single MSA tool consistently outperforms its counterparts across diverse datasets. Users often have to try multiple MSA tools to achieve optimal alignment results, which can be time-consuming and memory-intensive. While the overall accuracy of certain MSA results may be lower, there could be local regions with the highest alignment scores, prompting researchers to seek a tool capable of merging these locally optimal results from multiple initial alignments into a globally optimal alignment. In this study, we introduce Two Pointers Meta-Alignment (TPMA), a novel tool designed for the integration of nucleic acid sequence alignments. TPMA employs two pointers to partition the initial alignments into blocks containing identical sequence fragments. It selects blocks with the high sum of pairs (SP) scores to concatenate them into an alignment with an overall SP score superior to that of the initial alignments. Through tests on simulated and real datasets, the experimental results consistently demonstrate that TPMA outperforms M-Coffee in terms of aSP, Q, and total column (TC) scores across most datasets. Even in cases where TPMA's scores are comparable to M-Coffee, TPMA exhibits significantly lower running time and memory consumption. Furthermore, we comprehensively assessed all the MSA tools used in the experiments, considering accuracy, time, and memory consumption. We propose accurate and fast combination strategies for small and large datasets, which streamline the user tool selection process and facilitate large-scale dataset integration. The dataset and source code of TPMA are available on GitHub (https://github.com/malabz/TPMA).