OBJECTIVE: Femorotibial angle (FTA) is a convenient measure of coronal knee alignment that can be extracted from a short knee radiograph, avoiding the additional radiation exposure and specialist equipment required for full-leg radiographs. While intra- and inter-reader reproducibility from the same image has been reported, the full scan-rescan reproducibility across images, as calculated in this study, has not.
METHODS: In this study, 4589 FTA measurement pairs from 2586 subjects acquired a year apart were used to estimate FTA scan-rescan reproducibility using data from the Osteoarthritis Initiative. Subjects with radiographic progression of osteoarthritis or other conditions that may cause a change in coronal knee alignment were excluded. Measurement pairs were analysed using paired-samples  t $t$ tests to detect differences and compared to symptomatic changes in Western Ontario and McMaster Universities Arthritis Index scores for joint pain, stiffness and physical function to detect correlations.
RESULTS: The 95% limit of agreement and the paired-samples correlation were calculated with high precision to be [-1.76°, +1.78°] and 0.938, considerably worse than the corresponding figures for intra- and inter-reader reproducibility, without relation to symptomatic or radiographic changes in knee condition. This error will weakly attenuate R 2 ${R}^{2}$ and r $r$ values from their true values in correlative studies involving FTA. The realistic maximum value for R 2 ${R}^{2}$ is 87% and for Pearson\'s r $r$ is 93%.
CONCLUSIONS: The scan-rescan reproducibility in FTA is almost double the intra- and inter-reader reliability from a single scan. At almost ±2° accuracy, FTA is inappropriate for surgical use, but it is sufficiently reproducible to produce good correlations in studies predicting disease incidence and progression.
METHODS: Level II, retrospective study.

UNASSIGNED: The purpose of this study was to assess the differences in lower limb global alignment and anatomical parameters of coronal whole-leg radiographs, which were generally used in preoperative planning for high tibial osteotomy (HTO), according to different weight-bearing standing positions.
UNASSIGNED: Between April 2021 and December 2022, 176 patients (60 males and 116 females) were investigated. Full-weight-bearing coronal whole-leg radiographs were obtained with the patella centred on the femoral condyle. Patients were divided by Kellgren-Lawrence grade (KL-0, KL-I, KL-II and KL-III) and assessed in two standing positions: legs closed and legs spread. Patients with flexion contractures or those unable to stand with full weight bearing were excluded. The mechanical distal femoral angle, medial proximal tibial angle (MPTA), femorotibial angle, joint line convergence angle, percentage weight-bearing line (%WBL) and hip-knee-ankle angle (HKAA) were measured. The Student\'s t test was used to compare the two standing positions. A p value < 0.05 indicated a statistically significant difference.
UNASSIGNED: The MPTAs of legs closed standing and legs spread standing were 84.9 ± 2.6° and 85.1 ± 2.4° in KL-0, 84.7 ± 2.0° and 84.9 ± 2.1° in KL-I and 85.0 ± 2.43° and 85.4 ± 2.4° in KL-II, respectively. There were statistically significant differences in the MPTA between the two standing positions in KL-0, KL-I and KL-II. In contrast, the %WBL and HKAA did not change regardless of the standing position. In the KL-III group, no statistical significance was observed for any of the anatomical parameters.
UNASSIGNED: Several anatomical parameters were changed between the legs closed standing and the legs spread standing positions. It was suggested that the standing position should be taken into consideration in the planning for HTO.
UNASSIGNED: Level IV, Case series with no comparison group.

BACKGROUND: More personalized alignment techniques in total knee arthroplasty (TKA) have recently been described particularly for the young and active patients. Performing the ideal tibial cut might be challenging with a conventional ancillary. Therefore the aims of this study were: (1) to describe specific tibial landmarks to optimize the tibial cut in TKA; (2) to compare the accuracy of the tibial cut with these landmarks compared to a conventional technique.
METHODS: This retrospective case-control study compared primary TKAs performed using a conventional technique with extramedullary guide associated with specific tibial landmarks. For each case, one control patient was matched based on body mass index (BMI), age, preoperative Hip Knee Ankle (HKA) angle, and Medial Proximal Tibial Angle (MPTA). All control patients were operated by the same surgeon and similar conventional technique but without landmarks. The MPTA target was to reproduce preoperative deformity with a 3° of varus limit. 34 TKA were included in each group. There was no preoperative difference between both groups. Mean age was 63 years old ± 8. Mean BMI was 32 kg/m2 ± 5. Mean HKA was 170.6° ± 2.5. Mean MPTA was 85.1° ± 2.3. The radiographic assessment was performed preoperatively and at 2 months: HKA, mechanical Medial Distal Femoral Angle (mMDFA), MPTA, tibial slope, restoration of the joint line-height.
RESULTS: The tibial landmarks corresponded to the line of insertion of the deep medial collateral ligament fibers extended to the capsular insertion above the Gerdy tubercle. The postoperative MPTA was significantly more varus (87.2° ± 1.6 in landmark group versus 88.3° ± 2.2; p = 0.027) and closer to preoperative bone deformity in landmark group (p = 0.002) with significantly less outliers than in the conventional group. There was no significant difference between both groups postoperatively for HKA (175.4° ± 2.3 versus 175.9° ± 2.5; p = 0.42); mMDFA (88.9° ± 2.3 versus 88.2° ± 2.1; p = 0.18); tibial slope (82.6° ± 1.9 versus 82.4° ± 2.6; p = 0.67), the restoration of the joint line-height (1.5 mm ± 2 versus 1.8 mm ± 2; p = 0.56).
CONCLUSIONS: Specific tibial landmarks during TKA can be used to increase the accuracy of the tibial cut when using personalized alignment techniques in TKA.
METHODS: IV.

METHODS: This study was a retrospective multi-center comparative cohort study.
METHODS: A retrospective institutional database of operative adult spinal deformity patients was utilized. All fusions > 5 vertebral levels and including the sacrum/pelvis were eligible for inclusion. Revisions, 3 column osteotomies, and patients with < 2-year clinical follow-up were excluded. Patients were separated into 3 groups based on surgical approach: 1) posterior spinal fusion without interbody (PSF), 2) PSF with interbody (PSF-IB), and 3) anteroposterior (AP) fusion (anterior lumbar interbody fusion or lateral lumbar interbody fusion with posterior screw fixation). Intraoperative, radiographic, and clinical outcomes, as well as complications, were compared between groups with ANOVA and χ2 tests.
RESULTS: One-hundred and thirty-eight patients were included for study (PSF, n = 37; PSF-IB, n = 44; AP, n = 57). Intraoperatively, estimated blood loss was similar between groups (p = 0.171). However, the AP group had longer operative times (547.5 min) compared to PSF (385.1) and PSF-IB (370.7) (p < 0.001). Additionally, fusion length was shorter in PSF-IB (11.4) compared to AP (13.6) and PSF (12.9) (p = 0.004). There were no differences between the groups in terms of change in alignment from preoperative to 2 years postoperative. There were no differences in clinical outcomes. While postoperative complications were largely similar between groups, operative complications were higher in the AP group (31.6%) compared to the PSF (5.4%) and PSF-IB (9.1) groups (p < 0.001).
CONCLUSIONS: While there were differences in intraoperative outcomes (operative time and fusion length), there were no differences in postoperative clinical or radiographic outcomes. AP fusion was associated with a higher rate of operative complications.

Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that approximately 8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with metrics supporting a greater quality of the PacBio HiFi mCanLor1.2 assembly. Comparison between the wolf and other canine assemblies found that 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies.

Antibody sequences can be determined at 99% accuracy directly from the polypeptide product by using bottom-up proteomics techniques. Sequencing accuracy at the peptide level is limited by the isobaric residues leucine and isoleucine, incomplete fragmentation spectra in which the order of two or more residues remains ambiguous due to lacking fragment ions for the intermediate positions, and isobaric combinations of amino acids, of potentially different lengths, for example, GG = N and GA = Q. Here, we present several updates to Stitch (v1.5), which performs template-based assembly of de novo peptides to reconstruct antibody sequences. This version introduces a mass-based alignment algorithm that explicitly accounts for mass coincidence errors. In addition, it incorporates a postprocessing procedure to assign I/L residues based on secondary fragments (satellite ions, i.e., w-ions). Moreover, evidence for sequence assignments can now be directly evaluated with the addition of an integrated spectrum viewer. Lastly, input data from a wider selection of de novo peptide sequencing algorithms are allowed, now including Casanovo, PEAKS, Novor.Cloud, pNovo, and MaxNovo, in addition to flat text and FASTA. Combined, these changes make Stitch compatible with a larger range of data processing pipelines and improve its tolerance to peptide-level sequencing errors.

Background: In recent years, there has been considerable interest in prosthetic alignment techniques for total knee arthroplasty (TKA), particularly in the so-called kinematic alignment, which aims to restore the knee\'s native alignment. However, implementing this technique requires specialized instruments and procedural steps that can be laborious. This study introduces the bisector of the trochlear groove as a reliable landmark for performing the distal femoral cut while maintaining parallelism with the native femoral joint line. Methods: Three orthopedic specialists assessed 110 X-ray images of full-leg, weight-bearing lower limbs obtained from healthy individuals between January 2021 and December 2022. The bisector of the trochlear groove was identified on the X-ray images, and the angle between this bisector and the femoral joint line was measured. The consistency of these measurements across repeated assessments and different examiners was evaluated. Results: The bisector of the trochlear groove was found to be perpendicular to the femoral joint line, with a mean angle of 89.4°. The inter-rater reliability was 68% within ±1.3° from the mean, while the intra-rater reliability was 82% within ±1.5° from the mean. Conclusions: These results suggest that by performing a femoral cut perpendicular to the bisector of the trochlear groove, surgeons can inherently restore the femoral joint line of the native knee in patients where the native joint line is no longer identifiable due to the effect of osteoarthritis. This method may offer a viable and straightforward alternative to the standard surgical technique currently practiced for kinematic alignment in TKA.

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data (i.e. organizing data/metadata, applying image filters etc.) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI, a user interface for the well known tomography data processing package TomoPy. This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI, along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI, and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.

BACKGROUND: Cardiac safety assessment, such as lethal arrhythmias and contractility dysfunction, is critical during drug development. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have been shown to be useful in predicting drug-induced proarrhythmic risk through international validation studies. Although cardiac contractility is another key function, fit-for-purpose hiPSC-CMs in evaluating drug-induced contractile dysfunction remain poorly understood. In this study, we investigated whether alignment of hiPSC-CMs on nanopatterned culture plates can assess drug-induced contractile changes more efficiently than non-aligned monolayer culture.
METHODS: Aligned hiPSC-CMs were obtained by culturing on 96-well culture plates with a ridge-groove-ridge nanopattern on the bottom surface, while non-aligned hiPSC-CMs were cultured on regular 96-well plates. Next-generation sequencing and qPCR experiments were performed for gene expression analysis. Contractility of the hiPSC-CMs was assessed using an imaging-based motion analysis system.
RESULTS: When cultured on nanopatterned plates, hiPSC-CMs exhibited an aligned morphology and enhanced expression of genes encoding proteins that regulate contractility, including myosin heavy chain, calcium channel, and ryanodine receptor. Compared to cultures on regular plates, the aligned hiPSC-CMs also showed both enhanced contraction and relaxation velocity. In addition, the aligned hiPSC-CMs showed a more physiological response to positive and negative inotropic agents, such as isoproterenol and verapamil.
CONCLUSIONS: Taken together, the aligned hiPSC-CMs exhibited enhanced structural and functional properties, leading to an improved capacity for contractility assessment compared to the non-aligned cells. These findings suggest that the aligned hiPSC-CMs can be used to evaluate drug-induced cardiac contractile changes.

We developed two methods for three-dimensional (3D) evaluation of spinal alignment in standing position by image matching between biplanar x-ray images and 3D vertebral models. One used a Slot-Scanning 3D x-ray Imager (sterEOS) to obtain biplanar x-ray images, and the other used a conventional x-ray system and a rotating table. The 3D vertebral model was constructed from the CT scan data. The spatial position of the vertebral model was determined by minimizing the contour difference between the projected image of the model and the biplanar x-ray images. Verification experiments were conducted using a torso phantom. The relative positions of the upper vertebrae to the lowest vertebrae of the cervical, thoracic, and lumbar vertebrae were evaluated. The mean, standard deviation, and mean square error of the relative position were less than 1° and 1 mm in all cases for sterEOS. The maximum mean squared errors of the conventional x-ray system and the rotating table were 0.7° and 0.4 mm for the cervical spine, 1.0° and 1.2 mm for the thoracic spine, and 1.1° and 1.2 mm for the lumbar spine. Therefore, both methods could be useful for evaluating the spinal alignment in standing position.