Definition of anatomical zero positions for assessing shoulder pose with 3D motion capture during bilateral abduction of the arms

Background: Surgical interventions at the shoulder may alter function of the shoulder complex. Clinically, the outcome can be assessed by universal goniometry. Marker-based motion capture may not resemble these results due to differing angle definitions. Methods: The clinical inspection of bilateral arm abduction for assessing shoulder dysfunction is performed with a marker based 3D optical measurement method. An anatomical zero position of shoulder pose is proposed to determine absolute angles according to the Neutral-0-Method as used in orthopedic context. Static shoulder positions are documented simultaneously by 3D marker tracking and universal goniometry in 8 young and healthy volunteers. Repetitive bilateral arm abduction movements of at least 150° range of motion are monitored. Similarly a subject with gleno-humeral osteoarthritis is monitored for demonstrating the feasibility of the method and to illustrate possible shoulder dysfunction effects. Results: With mean differences of less than 2°, the proposed anatomical zero position results in good agreement between shoulder elevation/depression angles determined by 3D marker tracking and by universal goniometry in static positions. Lesser agreement is found for shoulder pro-/retraction with systematic deviations of up to 6°. In the bilateral arm abduction movements the volunteers perform a common and specific pattern in clavicula-thoracic and gleno-humeral motion with maximum shoulder angles of 32° elevation, 5° depression and 45° protraction, respectively, whereas retraction is hardly reached. Further, they all show relevant out of (frontal) plane motion with anteversion angles of 30° in overhead position (maximum abduction). With increasing arm anteversion the shoulder is increasingly retroverted, with a maximum of 20° retroversion. The subject with gleno-humeral osteoarthritis shows overall less shoulder abduction range of motion but with increased out-of-plane movement during abduction. Conclusions: The proposed anatomical zero definition for shoulder pose fills the missing link for determining absolute joint angles for shoulder elevation/depression and pro-/retraction. For elevation-/depression the accuracy suits clinical expectations very well with mean differences less than 2° and limits of agreement of 8.6° whereas for pro-/retraction the accuracy in individual cases may be inferior with limits of agreement of up to 24.6°. This has critically to be kept in mind when applying this concept to shoulder intervention studies

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

Background: Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. Results: Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. Conclusions: Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future

Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon

During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.We thank Dr. Daniel Cadar and Heike Baum from the NGS core facility of the Bernhard Nocht Institute for Tropical Medicine for technical support. We thank the Carl-Zeiss-Stiftung (FKZ 0563-2.8/738/2), TWMMG DigLeben (5575/10-9), and DFG iDIV (FZT 118, 202548816) for financial support. Figures were finalized with Inkscape v1.0.2.S

The International Virus Bioinformatics Meeting 2023

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting

Performance of stair negotiation in patients with cerebral palsy and stiff knee gait

Background Due to the limited knee range of motion, achieving adequate foot clearance while walking on level ground constitutes a major problem for patients with cerebral palsy and stiff knee gait. Stair negotiation as an activity of daily life requires a considerably higher knee range of motion than level ground walking, but little is known yet as to whether such patients are able to walk stairs. Research question: The aim of this study was to investigate how patients with a limited knee range of motion negotiate stairs. Do they increase their peak knee flexion and use the same pattern as in walking on level ground? How do the muscles act during stair negotiation? Methods In this explorative study, 17 adults with bilateral, spastic cerebral palsy and stiff knee gait and 25 healthy subjects were examined. 3D motion analysis, including electromyography, was performed while walking on level ground, upstairs, and downstairs. A linear mixed model was used for between- and within-group comparisons. Results Walking upstairs and downstairs, patients increased their peak knee flexion by around 30° compared to level walking. Thus, increased knee flexion may be seen as the main mechanism for maintaining foot clearance on stairs. An increased pelvic obliquity (elevation) and hip flexion were also found and involved subjects showed a slight increase in rectus femoris activity when walking on stairs compared to level walking within the phases of high knee flexion. Significance This study showed that patients with cerebral palsy and stiff knee gait are able to flex their knees more than would be required for level walking. Hence, the patients are able to adapt their rectus activity to stair walking to some extent. Therefore, further investigations might help to open up new therapeutic options to facilitate level walking and stair negotiation in patients with stiff knee gait

Effects of artificially induced bilateral internal rotation gait on gait kinematics and kinetics

BACKGROUND Bilateral internal rotation gait is a common gait abnormality in children with bilateral cerebral palsy, but still not fully understood. RESEARCH QUESTION The aim of this clinical study was to analyze the effects of artificially induced bilateral internal rotation gait on kinematics and kinetics. Our hypothesis was, that the internal rotation gait defined as increased dynamic internal hip rotation itself causes significant alterations in gait kinematics and kinetics. METHODS 30 typically developing children with a mean age of 12 (SD 3) years (range 8 - 16) performed three-dimensional gait analysis in two different conditions: with unaffected gait and with artificially induced bilateral internal rotation gait with two rotation bandages worn in order to internally rotate the hips. Kinematic and kinetic changes between these two conditions were calculated and compared using a mixed linear model with "gait condition" as fixed effect and both "limb" and "patient" as random effects. RESULTS The rotation bandages induced a significant increase in internal hip rotation and foot progression angle towards internal without affecting pelvic rotation. The peak hip internal rotator moment during loading response and the peak hip external rotator moment during the first half of stance phase increased significantly and the peak hip internal rotator moment during the second half of stance phase decreased significantly. Anterior pelvic tilt, hip flexion, knee flexion and ankle dorsiflexion increased significantly. The first peak of the frontal hip moment decreased, and the second increased significantly. The second peak of the frontal knee moment decreased significantly, while the first didn't change significantly. SIGNIFICANCE The data suggest, that the bilaterally increased dynamic internal hip rotation itself has a relevant impact on frontal hip moments. The increased anterior pelvic tilt, hip and knee flexion may be either induced by the pull of the rotation bandage or a secondary gait deviation

Supracondylar femoral rotation osteotomy affects frontal hip kinetics in children with bilateral cerebral palsy

AIM: To evaluate the influence of supracondylar femoral derotation osteotomy (FDO) on hip abduction muscle force and frontal hip moments in children with bilateral cerebral palsy. METHOD: For this retrospective cohort study 79 children (36 females, 43 males; mean age at surgery 11y [SD 3y]; range 4-17y) with bilateral cerebral palsy and preoperatively and 1-year postoperatively documented frontal hip moments who received supracondylar FDO in 134 limbs were included. The control group consisted of eight children (two females, six males; mean age 11y [SD 4y]; range 5-17y) who received single-event multi-level surgery without FDO. RESULTS: Hip joint impulse (p<0.001) and the first peak of frontal hip moments (p=0.003) increased, whereas the second peak decreased (p<0.001) from preoperatively to postoperatively. Hip abductor strength improved (p=0.001) from preoperatively to postoperatively. INTERPRETATION: Despite the compensatory mechanism, frontal hip moments are decreased preoperatively. Supracondylar FDO results in increased frontal hip moments. Changes in anteversion directly influence hip kinetics, although no direct change of the proximal bony geometry is performed

Metabolites of Key Flavor Compound 2,3,5-Trimethylpyrazine in Human Urine

Pyrazines are among the most important compound class conveying the odor impressions “roasty”, “nutty”, and “earthy”. They are formed by the Maillard reaction and occur ubiquitously in heated foods. The excretion of metabolites of the key flavor odorant 2,3,5-trimethylpyrazine, abundant in the volatile fraction of roasted coffee, was investigated. Based on literature suggestions, putative phase 1 and phase 2 metabolites were synthesized, characterized by nuclear magnetic resonance and mass spectroscopy data and used as standards for targeted, quantitative analysis of coffee drinkers’ urine using stable-isotope-dilution-ultrahigh-performance liquid chromatography tandem mass spectroscopy (SIDA-UHPLC–MS/MS). The analysis of spot urine samples from a coffee intervention study revealed 3,6-dimethylpyrazine-2-carboxylic acid, 3,5-dimethylpyrazine-2-carboxylic acid, and 5,6-dimethylpyrazine-2-carboxylic acid were quantitatively dominating metabolites. Only negligible traces of pyrazinemethanols (3,6-dimethyl-2-pyrazinemethanol and 3,5,6-trimethylpyrazine-2-ol), glucuronides ((3,6-dimethylpyrazine-2-yl-)methyl-O-β-D-glucuronide and (3,5-dimethylpyrazine-2-yl-)methyl-O-β-D-glucuronide), and sulfates ((3,6-dimethylpyrazine-2-yl-)methyl-sulfate and (3,5-dimethylpyrazine-2-yl-)methyl-sulfate) were detected

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

<div><p>The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes.</p></div