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Fungi, as eukaryotic organisms, contain two genomes, the mitochondrial genome and the nuclear genome, in their cells. How the two genomes evolve and correlate to each other is debated. Herein, taking the gourmet pine mushroom Tricholoma matsutake as an example, we performed comparative mitogenomic analysis using samples collected from diverse locations and compared the evolution of the two genomes. The T. matsutake mitogenome encodes 49 genes and is rich of repetitive and non-coding DNAs. Six genes were invaded by up to 11 group I introns, with one cox1 intron cox1P372 showing presence/absence dynamics among different samples. Bioinformatic analyses suggested limited or no evidence of mitochondrial heteroplasmy. Interestingly, hundreds of mitochondrial DNA fragments were found in the nuclear genome, with several larger than 500 nt confirmed by PCR assays and read count comparisons, indicating clear evidence of transfer of mitochondrial DNA into the nuclear genome. Nuclear DNA of T. matsutake showed a higher mutation rate than mitochondrial DNA. Furthermore, we found evidence of incongruence between phylogenetic trees derived from mitogenome and nuclear DNA sequences. Together, our results reveal the dynamic genome evolution of the gourmet pine mushroom.

The aim of this study was to determine age-related changes and sex-specific differences in sagittal alignment, range of motion (ROM), and intervertebral disc height of the thoracolumbar spine in healthy subjects. Lateral neutral and flexion–extension radiographs of the thoracolumbar spine of 627 asymptomatic subjects (307 males and 320 females; average age, 49.6 ± 16.5 years) were evaluated. We included at least 50 males and 50 females in each decade of life between the 20s and the 70s. Intervertebral disc height from T10/T11 to L5/S1, local lordotic alignment, and ROM from T10–T11 to L5–S1 were measured. T10–L2 kyphosis and T12–S1 lordosis as well as flexion, extension, and total ROM were measured. T10–L2 kyphosis did not markedly change with age in subjects of either sex but a sudden increase was noted in the 70s females. T12–S1 lordosis increased with age in both sexes, except the 70s. Flexion, extension, and total ROM at T10–L2 and T12–S1 decreased with age in most subjects. The levels from L3–L4 to L5–S1 were conspicuous as mobile segments. Intervertebral disc height gradually increased from T10/T11 to L4/L5; the shortest was at T10/T11 and the longest at L3/L4 or L4/L5 in all subjects. Age-related decreases in intervertebral disc height were most prominent at L4/L5 in middle-aged and elderly individuals of both sexes. Normative values of sagittal alignment, ROM, and intervertebral disc height at each segmental level were established in both sexes and all age groups in healthy subjects.

Background Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution. Results Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis. Conclusions Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies.

In a direction-giving task, we examine whether a high-level constraint—the task partners’ relative body alignment—influences spatial language use and task accuracy. In 32 pairs, task partners interacted in two conditions: for one route description, direction givers (DGs) and direction followers (DFs) sat side-by-side (aligned condition), and for another they sat opposite one another (counter-aligned condition). After each description, DFs drew the route on a map. When pairs were counter-aligned (vs. aligned), DGs increased their use of expressions from a survey perspective, using more frequently terms such as east-west. When counter-aligned, DFs also used more words per conversational turn, which was taken to reflect the increased difficulty of coordinating in that condition. Still, in terms of task performance, the accuracy of DFs’ drawings was unaffected by the partners’ body alignment or spatial language use it was only predicted by the DGs’ spatial ability. We argue that, because direction giving emphasizes accuracy, task partners invest in strategies that contribute to mutual understanding (e.g., recaps of the route by the DF at the end, evidenced by shifts in language use over time). Thus, body alignment in direction giving impacts coordination difficulty and spatial language use, but it does not singularly influence task performance. 57 2 99 121

The full-length standing radiograph in an anteroposterior projection is the primary tool for defining and measuring limb alignment with definition of the physiological axes and mechanical and anatomic angles of the lower limb. We define the deformities of the lower limb and the importance of correct surgical planning and execution. For patients with torsional malalignment of the lower limb, computerized tomography scan evaluation is the gold standard for preoperative assessment. Cite this article: EFORT Open Rev 2021;6:487-494. DOI: 10.1302/2058-5241.6.210015

Background The purpose of this study was to compare the degree of accuracy of coronal alignment correction with use of the “alignment adjustment under valgus stress technique” between expert and novice surgeons during medial opening-wedge high tibial osteotomy (MOWHTO). Methods Forty-eight patients who underwent MOWHTO performed by an expert surgeon (expert group) and 29 by a novice surgeon (novice group) were enrolled in analysis. During surgery, lower-extremity alignment was corrected using the “alignment adjustment under valgus stress technique”. Normocorrection was defined as a weight-bearing line ratio between 55 and 70% and the correction accuracy was compared between expert and novice groups using the ratio of normocorrection to outliers. The clinical outcomes were also compared using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) at 1 year after surgery. Results The undercorrection rate was 14.6% in the expert group and 13.8% in the novice group, while the overcorrection rate was 2.1% in the expert group and 3.4% in the novice group. In the ratio of normocorrection to outliers, no difference was found between the two groups at the one-year follow-up visit (83.3% in the expert group vs. 82.8% in the novice group; p > 0.05). Also, no significant differences were seen in WOMAC subscores immediately preoperatively and at 1 year after surgery (all p > 0.05). Conclusion Adhering to the “alignment adjustment under valgus stress technique” protocol enabled novice surgeons to achieve similar surgical accuracy as that of an expert surgeon in coronal alignment during MOWHTO. Level of evidence Level III.

The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 26 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content, genome organization, and inverted repeat contraction and expansion comprising 113 genes, including 80 protein‐coding, 29 transfer RNA, and 4 ribosomal RNA genes. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16‐trnQ, ycf1, ndhF‐rpl32, petN‐psbM, and rpl32‐trnL, and they may be suitable for the development of robust, authentic, and cost‐effective markers for barcoding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co‐occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. At tribe level, our phylogeny supports a sister relationship between Astereae and Anthemideae rooted as Gnaphalieae, Calenduleae, and Senecioneae. These results are contradictory to recent studies which reported a sister relationship between “Senecioneae and Anthemideae” and “Astereae and Gnaphalieae” or a sister relationship between Astereae and Gnaphalieae rooted as Calenduleae, Anthemideae, and then Senecioneae using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between plastidt and nuclear genome data require further investigation.

Resumen Introducción: El objetivo de este estudio es describir la morfología del retropié mediante cortes coronales con tomografía computarizada en pacientes con coaliciones tarsianas. Materiales y Métodos: Se incluyeron 85 pies de 78 pacientes de entre 9 y 17 años. Fueron divididos en 3 grupos: 1) grupo de control (n = 29), 2) con coaliciones calcáneo-escafoideas (CCE) (n = 31) y 3) con coaliciones astrágalo-calcáneas (CAC) (n = 25). Dos observadores valoraron cinco medidas: Inftal-Suptal, Inftal-Hor, Inftal-Supcal, Suptal-Infcal y el ángulo astrágalo-calcáneo (AAC). Resultados: Los grupos no presentaron diferencias en la distribución por edad y sexo. Los pacientes con coaliciones tarsianas tuvieron valores significativamente superiores en todas las mediciones comparados con el grupo de control (p

Background:The effect of high tibial osteotomy (HTO) on the stress distribution across the knee joint is not completely understood. Subchondral bone density is considered to reflect the pattern of stress distribution across a joint surface.Purpose:To assess the distribution of subchondral bone density across the proximal tibia in nonarthritic knees and in the knees of patients with osteoarthritis (OA) before and after HTO.Study Design:Cohort study; Level of evidence, 3.Methods:We retrospectively collected radiological and computed tomography data from 16 patients without OA (control group) and 17 patients with OA. Data from the OA group were collected before and 1.5 years after HTO. Subchondral bone density of the proximal tibia was assessed with computed tomography–osteoabsorptiometry. The locations and percentages represented by high-density areas (HDAs) on the articular surface were quantitatively analyzed.Results:The ratio of the HDA of the medial compartment to the total HDA (medial ratio) was significantly higher in the preoperative OA group (mean, 80.1%) than in the control group (61.3%) ( P < .001). After HTO, the medial ratio decreased significantly to 75.1% ( P = .035 in comparison with preoperative values) and was significantly correlated with the hip-knee-ankle angle in both groups: control ( r = −0.551; P = .033) and OA ( r = −0.528; P = .043). The change in medial ratio after HTO was significantly correlated with the change in hip-knee-ankle angle ( r = 0.587; P = .035). In the medial compartment, the HDA in the most lateral region of 4 subregions increased after HTO, but that in 3 medial subregions decreased.Conclusion:In this exploratory study, HTO shifted the HDA of the medial compartment of the proximal tibial articular surface toward the lateral compartment. In contrast, the HDA of the most lateral region of the medial compartment increased after HTO. This change in subchondral bone density may result from the change in stress distribution.

Background Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow a consistent data analysis pipeline to achieve the highest possible accuracy and avoid false variant calls. Herein, we aimed to compare the performance of twenty-eight combinations of NGS data analysis pipeline compartments, including short-read mapping (BWA-MEM, Bowtie2, Stampy), variant calling (GATK-HaplotypeCaller, GATK-UnifiedGenotyper, SAMtools) and interval padding (null, 50 bp, 100 bp) methods, along with a commercially available pipeline (BWA Enrichment, Illumina®). Fourteen germline DNA samples from breast cancer patients were sequenced using a targeted NGS panel approach and subjected to data analysis. Results We highlight that interval padding is required for the accurate detection of intronic variants including spliceogenic pathogenic variants (PVs). In addition, using nearly default parameters, the BWA Enrichment algorithm, failed to detect these spliceogenic PVs and a missense PV in the TP53 gene. We also recommend the BWA-MEM algorithm for sequence alignment, whereas variant calling should be performed using a combination of variant calling algorithms; GATK-HaplotypeCaller and SAMtools for the accurate detection of insertions/deletions and GATK-UnifiedGenotyper for the efficient detection of single nucleotide variant calls. Conclusions These findings have important implications towards the identification of clinically actionable variants through panel testing in a clinical laboratory setting, when dedicated bioinformatics personnel might not always be available. The results also reveal the necessity of improving the existing tools and/or at the same time developing new pipelines to generate more reliable and more consistent data.

Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

AimsThe purpose of this study was to compare the radiological outcomes of manual versus robotic-assisted medial unicompartmental knee arthroplasty (UKA).MethodsPostoperative radiological outcomes from 86 consecutive robotic-assisted UKAs (RAUKA group) from a single academic centre were retrospectively reviewed and compared to 253 manual UKAs (MUKA group) drawn from a prior study at our institution. Femoral coronal and sagittal angles (FCA, FSA), tibial coronal and sagittal angles (TCA, TSA), and implant overhang were radiologically measured to identify outliers.ResultsWhen assessing the accuracy of RAUKAs, 91.6% of all alignment measurements and 99.2% of all overhang measurements were within the target range. All alignment and overhang targets were simultaneously met in 68.6% of RAUKAs. When comparing radiological outcomes between the RAUKA and MUKA groups, statistically significant differences were identified for combined outliers in FCA (2.3% vs 12.6%; p = 0.006), FSA (17.4% vs 50.2%; p < 0.001), TCA (5.8% vs 41.5%; p < 0.001), and TSA (8.1% vs 18.6%; p = 0.023), as well as anterior (0.0% vs 4.7%; p = 0.042), posterior (1.2% vs 13.4%; p = 0.001), and medial (1.2% vs 14.2%; p < 0.001) overhang outliers.ConclusionRobotic system navigation decreases alignment and overhang outliers compared to manual UKA. Given the association between component placement errors and revision in UKA, this strong significant improvement in accuracy may improve implant survival. Level of Evidence: III Cite this article: Bone Jt Open 2021;2-3:191–197.

PurposeThe aim of this study is to investigate the prognostic value of tibial component coverage (over-hang and under-hang) and the alignment of total knee arthroplasty (TKA) components 1 week after surgery. We select patient-reported outcome measures (PROMS) (the Knee Society score (KSS score) and the Western Ontario and McMaster Universities Osteoarthritis Index-pain score (WOMAC pain score)) and tibial bone resorption (TBR) 2 years after surgery as the end points.MethodsThe study retrospectively analyzed 109 patients undergoing TKA (fixed-bearing prosthesis with asymmetrical tibial tray) from January 2014 to December 2017 in Huashan Hospital. By using standard long-leg X-rays, anteroposterior (AP) and lateral X-rays of the knee, tibial component coverage (under-hang or over-hang), AP tibial-femoral anatomical angle (AP-TFA), AP femoral angle (AP-FA), AP tibial angle (AP-TA), and lateral tibial angle (L-TA) were measured at 1 week after surgery, while TBR was measured through postoperative 1-week and 2-year AP and lateral radiographs of the knee on three sides (medial side, lateral side on AP radiograph, and anterior side on lateral radiograph). The Pearson correlation analysis, simple linear regression, multiple linear regression, the Student’sttest, and one-way ANOVA together with Tukey’s post hoc test (or Games-Howell post hoc test) were used in the analyses.ResultsTibial under-hang was more likely to appear in our patients following TKA (42%, medially, 39%, laterally, and 25%, anteriorly). In multivariate linear regression analysis of TBR, tibial under-hang (negative value) 1 week after surgery was positively correlated with TBR 2 years later on the medial (p= 0.003) and lateral (p= 0.026) side. Tibial over-hang (positive value) 1 week after surgery on the medial side was found negatively related with KSS score (p= 0.004) and positively related with WOMAC pain score (p= 0.036) 2 years later in multivariate linear regression analysis of PROMS. Both scores were better in the anatomically sized group than in the mild over-hang group (or severe over-hang) (p< 0.001). However, no significant relationship was found between the alignment of TKA components at 1 week after surgery and the end points (TBR and PROMS) 2 years later.ConclusionUnder-hang of the tibial component on both the medial and lateral sides can increase the risk of TBR 2 years later. Over-hang of tibial component on the medial side decreases the PROMS (KSS score and WOMAC pain score) 2 years later. An appropriate size of tibial component during TKA is extremely important for patient’s prognosis, while the alignment of components might not be as important.

Background: Asymmetry analysis of retinal layers in right and left eyes can be a valuable tool for early diagnoses of retinal diseases. To determine the limits of the normal interocular asymmetry in retinal layers around macula, thickness measurements are obtained with optical coherence tomography (OCT). Methods: For this purpose, after segmentation of intraretinal layer in threedimensional OCT data and calculating the midmacular point, the TM of each layer is obtained in 9 sectors in concentric circles around the macula. To compare corresponding sectors in the right and left eyes, the TMs of the left and right images are registered by alignment of retinal raphe (i.e. diskfovea axes). Since the retinal raphe of macular OCTs is not calculable due to limited region size, the TMs are registered by first aligning corresponding retinal raphe of fundus images and then registration of the OCTs to aligned fundus images. To analyze the asymmetry in each retinal layer, the mean and standard deviation of thickness in 9 sectors of 11 layers are calculated in 50 normal individuals. Results: The results demonstrate that some sectors of retinal layers have signifcant asymmetry with P < 0.05 in normal population. In this base, the tolerance limits for normal individuals are calculated. Conclusion: This article shows that normal population does not have identical retinal information in both eyes, and without considering this reality, normal asymmetry in information gathered from both eyes might be interpreted as retinal disorders.

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling., We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and the University of York. We thank David K. James and Lucia Hui of the Alameda County Vector Control Services District for procuring the rat used for the de novo genome. We are grateful to Sarah Nagel at Max Planck Institute for the Evolutionary Anthropology for the single-stranded library preparation, and Dovetail Genomics for the de novo genome assembly service. We thank Maria Spyrou for her suggestions and comments. We acknowledge Ewan Chipping and Helena England (University of York), Carl Phillips, Veronica Lindholm (Ålands Museum), Christine McDonnell and Nienke van Doorn (York Archaeological Trust), Emile Mittendorf (Gemeente Deventer), Inge Riemersma (Archaeological depot, Provincie Zuid-Holland), the Turkish Ministry of Culture & Tourism, Jan Frolík and Iva Herichová (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Nyékhelyi and László Daróczi-Szabó (Budapest History Museum), Institut National du Patrimoine (Tunisia), University of Barcelona, Spanish Ministry of Science and Innovation (Project HUM2006-03432/HIST), Spanish Ministry of Culture (program of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vujadin Ivanisević, Nemanja Marković and Ivan Bugarski (Archaeological Institute 809 Belgrade), the Field Museum Chicago, the British National History Museum and the American Museum of Natural History for providing materials and support. G.L. and A.J. were supported by the ERC (grant ERC-2013-StG-337574-UNDEAD) and A.J. was supported by the Natural Environment Research Council Doctoral Training Program. D.O. was supported by Wellcome (Small Grant in Humanities and Social Science 209817/Z) and the British Academy / Leverhulme Trust (Small Research Grant SG170938). E.R. was supported by Estonian Research Council grant No PRG29. R.K. was supported by the Czech Academy of Sciences institutional support (RVO:67985912). S.V.-L. was supported by the ERC (grant ERC-StG- 716298 ZooMWest). H.E. was funded by an ERC grant (206148) through the Sealinks Project. A.H.B was funded by the Leverhulme Trust (ECF-2017-315). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society.

Background: Difference in the clinical course and outcomes between simultaneous- and staged-bilateral medial opening wedge high tibial osteotomies (OWHTOs) over time was unknown. The study hypothesis was that patients who underwent simultaneous-bilateral OWHTO (SMBO) have a more rapid improvement in knee function than those who underwent staged-bilateral OWHTO (STBO) due to difference in the change of lower limb alignment between SMBO and STBO. Methods: The records of 56 knees in 28 patients who underwent either SMBO (n = 28) or STBO (n = 28) were retrospectively analysed. The time course data of weight-bearing line percentage (%WBL), joint line convergence angle (JLCA), and Knee Society Score were compared between the two procedures. Results: Hospitalisation for SMBO was longer than that for STBO by 1 week. No significant difference was observed in %WBL between the two procedures. The JLCA was significantly lower with SMBO than with the first-stage surgery of STBO (P

Introduction In the hub and spoke laboratory network, the number of hematology analyzers (HAs) within each core center has increased, and the control of HAs alignment is becoming necessary requirement to ensure analytical quality. In this scenario, HA alignment can be assessed by analyzing the same control material used for internal quality control on multiple HAs, assuming its commutability. The aim of the study was to verify the applicability of a protocol for the alignment of HAs based on control material rather than on fresh whole-blood samples. Methods The alignment of five HAs was evaluated for red (RBC, Hb, MCV, RET), white (WBC, NE, LY, MO, EO, BA, IG), and platelet (PLT) series parameters, following a protocol by SIBioC, using human sample (HS) and quality control material (QC), after the verification of commutability, according to the IFCC protocol. Maximum bias was derived from biological variation data. Results A complete alignment between instruments was confirmed for the majority of the parameters investigated both for HS and QC material. Partial misalignments or inconcludent results were instead evident for MCV, MO, EO, BA, and IG. Interestingly, QC material was found to be not commutable for LY, MO, and BA. Conclusion The alignment of hematologic analyzers for main cell population parameters may be verified with both QC and HS, displaying consistent results and interpretation. The evaluation for some white series parameters (EO, BA, and IG) is critical, and particular attention must be paid to the values of the material used for the alignment.

Short stems are becoming increasingly popular in total hip arthroplasty as they preserve the bone stock and simplify the implantation process. Short stems are advised mainly for patients with good bone stock. The clinical use of short stems could be enlarged to patients with poor bone stock if a cemented alternative would be available. Therefore, this study aimed to quantify the mechanical performance of a cemented short stem and to compare the "undersized" cementing strategy (stem one size smaller than the rasp) with the "line-to-line" technique (stem and rasp with identical size). A prototype cemented short stem was implanted in eight pairs of human cadaveric femora using the two cementing strategies. Four pairs were experimentally tested in a single-legged stance condition; stiffness, strength, and bone surface displacements were measured. Subject-specific nonlinear finite element models of all the implanted femora were developed, validated against the experimental data, and used to evaluate the behavior of cemented short stems under physiological loading conditions resembling level walking. The two cementing techniques resulted in nonsignificant differences in stiffness and strength. Strength and stiffness as calculated from finite element were 8.7 ± 16% and 9.9 ± 15.0% higher than experimentally measured. Displacements as calculated from finite element analyses corresponded strongly (R 2 ≥ .97) with those measured by digital image correlation. Stresses during level walking were far below the fatigue limit for bone and bone cement. The present study suggests that cemented short stems are a promising solution in osteoporotic bone, and that the line-to-line and undersized cementing techniques provide similar outcomes. ispartof: JOURNAL OF ORTHOPAEDIC RESEARCH vol:39 issue:8 pages:1681-1690 ispartof: location:United States status: published

The aim of this study was to estimate whether kinematic alignment (KA) improves knee function or clinical outcomes compared with mechanical alignment (MA) in the short term after total knee arthroplasty (TKA). We searched the literature for randomized controlled trials published before January 2020 from PubMed, EMBASE, Google, Web of Science, Cochrane Library, and other databases. The observation markers included “The Western Ontario and McMaster Universities (WOMAC) Osteoarthritis Index,” “Knee Society Score (KSS),” “Oxford Knee Score (OKS),” “combined Knee Society Score (KSS),” “Knee injury and Osteoarthritis Outcome Score (KOOS),” “European Quality of Life Measure‐5 Domain‐5‐Level (EQ‐5D‐5L),” range of motion (ROM), lower limb alignment, ligament release, and complications. A total of 11 randomized controlled trial studies were included in the study. During the follow‐up of 6–24 months, the KA‐TKA group was superior to the MA‐TKA group in terms of WOMAC scores, combined KSS, KSS, knee function scores, and knee range of flexion, but there was no significant difference in EQ‐5D‐5L, KOOS, KOOS (symptoms, pain, ADL, sports, and quality of life), complications, knee range of extension, hip‐knee‐ankle (HKA) angle, tibial component slope angle, lateral distal femoral angle (LDFA) or medial proximal tibial angle (MPTA) angle between the MA‐TKA group and the MA‐TKA group (P > 0.05). Our meta‐analysis revealed that the incidence of ligament release in the MA‐TKA group was higher than that in the KA‐TKA group. This meta‐analysis shows that the KA‐TKA group had better clinical outcomes and knee range of flexion than the MA‐TKA group at short‐term follow‐up., Although the survival rate of MA‐TKA has improved, approximately 20%–25% of patients remain unsatisfied with the outcome.Therefore, this article to evaluate whether the clinical outcome of KA‐TKA is better than that of MA‐TKA.

Background: The cause of Alzheimer’s disease (AD) is poorly understood. Neurotropic microbes, particularly herpesviruses, might set off chronic neuroinflammation. Amyloid-β (Aβ) has antimicrobial properties and could represent a brain defense against infection. Objective: We searched for protein sequence alignment between herpes simplex virus type I (HSV-1) HSV-2, and Aβ. Methods: Protein data bank (pdb) structures for Aβ, HSV-1, and HSV-2 were searched on the RCSB Protein Data Bank. The protein structures were superimposed and aligned on PYMOL v 2.3.4. Results: For HSV-1 and Aβ, amino acid residues ser549 – his569 of HSV-1 aligned closely with residues asp7 - asn27 of Aβ. For HSV-2 and Aβ, amino acid residues of HSV-2 aligned less closely than those of HSV-1 with residues of Aβ. Conclusion: Conjugating and binding to the same alpha helix in the HSV-1 protease, Aβ could be marking HSV-1 for attack by the immune system, providing a rapid inherited immune response to a destructive neurotropic virus that would otherwise require the more time-consuming involvement of T-cells, B-cells, and the adaptive immune system. But older people do not respond to viral infections as well as younger individuals. When HSV-1 infection advances in an old person, more and more amyloid is produced, forming an adhesive web. As the brain tries to hold the pathologic process in check, neuroinflammation increases and spreads. Progressive neurodegeneration and cognitive decline are the outcome.

Summary Typical RNA sequencing (RNA-Seq) analyses are performed either at the gene level by summing all reads from the same locus, assuming that all transcripts from a gene make a protein or at the transcript level, assuming that each transcript displays unique function. However, these assumptions are flawed, as a gene can code for different types of transcripts and different transcripts are capable of synthesizing similar, different or no protein. As a consequence, functional changes are not well illustrated by either gene or transcript analyses. We propose to improve RNA-Seq analyses by grouping the transcripts based on their similar functions. We developed FuSe to predict functional similarities using the primary and secondary structure of proteins. To estimate the likelihood of proteins with similar functions, FuSe computes two confidence scores: knowledge (KS) and discovery (DS) for protein pairs. Overlapping protein pairs exhibiting high confidence are grouped to form ‘similar function protein groups’ and expression is calculated for each functional group. The impact of using FuSe is demonstrated on in vitro cells exposed to paracetamol, which highlight genes responsible for cell adhesion and glycogen regulation which were earlier shown to be not differentially expressed with traditional analysis methods. Availability and implementation The source code is available at https://github.com/rajinder4489/FuSe. Data for APAP exposure are available in the BioStudies database (http://www.ebi.ac.uk/biostudies) under accession numbers S-HECA143, S-HECA(158) and S-HECA139. Supplementary information Supplementary data are available at Bioinformatics online.

Background The alignment of human lower limb has been an area of ongoing study for decades. The purpose of this study was to analyze the axial and rotational alignment from hip to ankle in a Caucasian aged non-arthritic cohort. Methods A non-arthritic cohort of aged patients was retrospectively analyzed by computer tomography. Anatomical–mechanical angle of femur (AMA), femur inclination (FI), femoral anteversion (FA), posterior condylar angle (PCA), proximal tibial torsion (TEAs-PTC and TEAs-PTT) and tibial fibular torsion (PTC-TFA) were measured. Results The median age of the patients was 76 years (range 67 to 91 years). Regarding axial alignment, the AMA was 5 (2.94; 6.80). No significance differences were reported by side and age. AMA was significantly lower in men. The FI was 125.3 (120.0; 134.8) with no differences in terms of side, age or gender. Regarding torsion alignment, the median values of FA, PTC-TFA and TEAs-PTT were, respectively, 16.8, 28.5 and − 1.4. No differences were reported by age. Right tibia was externally rotated by 1.5 degrees as compared to the left side (P 0.035). Conclusion The broad variability of the parameters analyzed highlights the necessity for a more anatomical and individualized approach during surgery of lower limb. The present study offers the fundament to understand and treat lower limb deformities. Hence, these data can constitute the normal reference values useful to investigate lower limb malalignment. Moreover, it helps to assess the possible changes of axial and rotational alignment in idiopathic OA of lower limb. Level of evidence III Retrospective cohort study

BackgroundA method that can accurately predict the outcome of surgery can give patients timely feedback. In addition, to some extent, an objective evaluation method can help the surgeon quickly summarize the patient’s surgical experience and lessen dependence on the long wait for follow-up results. However, there was still no precise tool to predict clinical outcomes of total knee arthroplasty (TKA). This study aimed to develop a scoring system to predict clinical results of TKA and then grade the quality of TKA.MethodsWe retrospectively reviewed 98 primary TKAs performed between April 2013 and March 2017 to determine predictors of clinical outcomes among lower-extremity angles of alignment. Applying multivariable linear-regression analysis, we built Models (i) and (ii) to predict detailed clinical outcomes which were evaluated using the Knee Society Score (KSS). Multivariable logistic-regression analysis was used to establish Model (iii) to predict probability of getting a good clinical outcome (PGGCO) which was evaluated by Knee Injury and Osteoarthritis Outcome Score (KOOS) score. Finally, we designed a new scoring system consisting of 3 prediction models and presented a method of grading TKA quality. Thirty primary TKAs between April and December 2017 were enrolled for external validation.ResultsWe set up a scoring system consisting of 3 models. The interpretations of Model (i) and (ii) were good (R2 = 0.756 and 0.764, respectively). Model (iii) displayed good discrimination, with an area under the curve (AUC) of 0.936, and good calibration according to the calibration curve. Quality of surgery was stratified as follows: “A” = PGGCO ≥0.8, “B” = PGGCO ≤0.6 but ConclusionsThis study first developed a validated, evidence-based scoring system based on lower-extremity angles of alignment to predict early clinical outcomes and to objectively evaluate the quality of TKA.

Although mechanical alignment (MA) has traditionally been considered the gold standard, the optimal alignment strategy for total knee arthroplasty (TKA) is still debated. Kinematic alignment (KA) aims to restore native alignment by respecting the three axes of rotation of the knee and thereby producing knee motion more akin to the native knee. Designer surgeon case series and case control studies have demonstrated excellent subjective and objective clinical outcomes as well as survivorship for KA TKA with up to 10 years follow up, but these results have not been reproduced in high-quality randomized clinical trials. Gait analyses have demonstrated differences in parameters such as knee adduction, extension and external rotation moments, the relevance of which needs further evaluation. Objective improvements in soft tissue balance using KA have not been shown to result in improvements in patient-reported outcomes measures. Technologies that permit accurate reproduction of implant positioning and objective measurement of soft tissue balance, such as robotic-assisted TKA and compartmental pressure sensors, may play an important role in improving our understanding of the optimum alignment strategy and implant position.Cite this article: EFORT Open Rev 2020;5:486-497. DOI: 10.1302/2058-5241.5.190093

In this paper we present an updated checklist of thallus-forming Laboulbeniomycetes (Ascomycota, Pezizomycotina), that is, the orders Herpomycetales and Laboulbeniales, from Belgium and the Netherlands. Two species are newly described based on morphology, molecular data (ITS, LSU ribosomal DNA) and ecology (host association). These areHesperomyces halyziaeonHalyzia sedecimguttata(Coleoptera, Coccinellidae) from both countries andLaboulbenia quarantenaeonBembidion biguttatum(Coleoptera, Carabidae) from Belgium. In addition, nine new country records are presented. For Belgium:Laboulbenia aubryionAmara aranea(Coleoptera, Carabidae) andRhachomyces spinosusonSyntomus foveatus(Coleoptera, Carabidae). For the Netherlands:Chitonomyces melanurusonLaccophilus minutus(Coleoptera, Dytiscidae),Euphoriomyces agathidiionAgathidium laevigatum(Coleoptera, Leiodidae),Laboulbenia fasciculataonOmophron limbatum(Coleoptera, Carabidae),Laboulbenia metabletionSyntomus foveatusandS. truncatellus(Coleoptera, Carabidae),Laboulbenia pseudomaseionPterostichus melanarius(Coleoptera, Carabidae),Rhachomyces canariensisonTrechus obtusus(Coleoptera, Carabidae), andStigmatomyces hydrelliaeonHydrellia albilabris(Diptera, Ephydridae). Finally, an identification key to 140 species of thallus-forming Laboulbeniomycetes in Belgium and the Netherlands is provided. Based on the combined data, we are able to identify mutual gaps that need to be filled as well as weigh the impact of chosen strategies (fieldwork, museum collections) and techniques in these neighboring countries. The aim of this work is to serve as a reference for studying Laboulbeniomycetes fungi in Europe.

BackgroundDespite many efforts to achieve better coordination, fragmentation is an enduring feature of the global health landscape that undermines the effectiveness of health programmes and threatens the attainment of the health-related Sustainable Development Goals. In this paper we identify and describe the multiple causes of fragmentation in development assistant for health at the global level. The study is of particular relevance since the emergence of new global health problems such as COVID-19 heightens the need for global health actors to work in coordinated ways. Our study is part of theLancet Commission on Synergies between Universal Health Coverage, Health Security and Health Promotion.MethodsWe used a mixed methods approach. This consisted of a non-systematic literature review of published papers in scientific journals, reports, books and websites. We also carried out twenty semi-structured expert interviews with individuals from bilateral and multilateral organisations, governments and academic and research institutions between April 2019 and December 2019.ResultsWe identified five distinct yet interconnected sets of factors causing fragmentation: proliferation of global health actors; problems of global leadership; divergent interests; problems of accountability; problems of power relations. We explain why global health actors struggle to harmonise their approaches and priorities, fail to align their work with low- and middle-income countries’ needs and why they continue to embrace funding instruments that create fragmentation.ConclusionsMany global actors are genuinely committed to addressing the problems of fragmentation, despite their complexity and interconnected nature. This paper aims to raise awareness and understanding of the causes of fragmentation and to help guide actors’ efforts in addressing the problems and moving to more synergistic approaches.

Background The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly. Results We propose OpticalKermit which directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler, OpticalKermit produces an assembly with almost three times higher NGA50 with a lower number of misassemblies on real A. thaliana reads. Conclusions OpticalKermit successfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.

In patients with metastatic cancer, gut microbiome composition differs between responder and non-responders to immune checkpoint inhibitors. However, there is little consensus on the microbiome taxa associated with response or lack of response. Additionally, recognized confounders of gut microbiome composition have generally not been taken into account. In this study, metagenomic shotgun sequencing was performed on freshly frozen pre-treatment stool samples from 25 patients (12 responders and 13 non-responders) with unresectable metastatic melanoma treated with immune checkpoint inhibitors. We observed no significant differences in alpha-diversity and bacterial prevalence between responders and non-responders (P > 0.05). In a zero-inflated multivariate analysis, correcting for important confounders such as age, BMI and use of antibiotics, 68 taxa showed differential abundance between responders and non-responders (false-discovery rate

Alignment of scRNA-Seq data are the first and one of the most critical steps of the scRNA-Seq analysis workflow, and thus the choice of proper aligners is of paramount importance. Recently, STAR an alignment method and Kallisto a pseudoalignment method have both gained a vast amount of popularity in the single cell sequencing field. However, an unbiased third-party comparison of these two methods in scRNA-Seq is lacking. Here we conduct a systematic comparison of them on a variety of Drop-seq, Fluidigm and 10x genomics data, from the aspects of gene abundance, alignment accuracy, as well as computational speed and memory use. We observe that STAR globally produces more genes and higher gene-expression values, compared to Kallisto, as well as Bowtie2, another popular alignment method for bulk RNA-Seq. STAR also yields higher correlations of the Gini index for the genes with RNA-FISH validation results. Using 10x genomics PBMC 3K scRNA-Seq and mouse cortex single nuclei RNA-Seq data, STAR shows similar or better cell-type annotation results, by detecting a larger subset of known gene markers. However, the gain of accuracy and gene abundance of STAR alignment comes with the price of significantly slower computation time (4 folds) and more memory (7.7 folds), compared to Kallisto.

Tissue-engineered constructs have great potential in many intervention strategies. In order for these constructs to function optimally, they should ideally mimic the cellular alignment and orientation found in the tissues to be treated. Here we present a simple and reproducible method for the production of cell-laden pure fibrin micro-fibers with longitudinal topography. The micro-fibers were produced using a molding technique and longitudinal topography was induced by a single initial stretch. Using this method, fibers up to 1 m in length and with diameters of 0.2-3 mm could be produced. The micro-fibers were generated with embedded endothelial cells, smooth muscle cell/fibroblasts or Schwann cells. Polarized light and scanning electron microscopy imaging showed that the initial stretch was sufficient to induce longitudinal topography in the fibrin gel. Cells in the unstretched control micro-fibers elongated randomly in both the floating and encapsulated environments, whereas the cells in the stretched micro-fibers responded to the introduced topography by adopting a similar orientation. Proof of concept bottom-up tissue engineering (TE) constructs are shown, all displaying various anisotropic organization of cells within. This simple, economical, versatile and scalable approach for the production of highly orientated and cell-laden micro-fibers is easily transferrable to any TE laboratory.

Background GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions. Results We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Since March 2020, VADR has also been used to check SARS-CoV-2 sequence submissions. Other viruses with high numbers of submissions will be added incrementally. Conclusion VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allow researchers to run the GenBank checks prior to submitting their viral sequences, and thereby gain confidence that their submissions will be accepted immediately without the need to correspond with GenBank staff. Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than checking routine viral sequence submissions.

Honey bees (Apis mellifera) produce an enormous economic value through their pollination activities and play a central role in the biodiversity of entire ecosystems. Recent efforts have revealed the substantial influence that the gut microbiota exert on bee development, food digestion, and homeostasis in general. In this study, deep sequencing was used to characterize prokaryotic viral communities associated with honey bees, which was a blind spot in research up until now. The vast majority of the prokaryotic viral populations are novel at the genus level, and most of the encoded proteins comprise unknown functions. Nevertheless, genomes of bacteriophages were predicted to infect nearly every major bee-gut bacterium, and functional annotation and auxiliary metabolic gene discovery imply the potential to influence microbial metabolism. Furthermore, undiscovered genes involved in the synthesis of secondary metabolic biosynthetic gene clusters reflect a wealth of previously untapped enzymatic resources hidden in the bee bacteriophage community. ispartof: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA vol:117 issue:19 pages:10511-10519 ispartof: location:United States status: published

A considerable proportion of patients (19%) are dissatisfied after total knee arthroplasty (TKA). Possible factors contributing to this dissatisfaction are decreased posterior condylar offset (PCO) with subsequent joint line elevation, leading to mid-flexion instability. Secondly, the pre-disease mechanical alignment is changed into a neutral alignment. The Flexion First Balancer was developed to avoid these problems. This technique aims to maintain MCL isometry by restoring medial PCO and medial joint line to its pre-disease level. Also, to reconstruct the pre-disease mechanical alignment by adjusting the distal femoral angle. In this study we provide a detailed technical overview of the Flexion First Balancer technique.

Background DNA sequencing is at the core of many molecular biology laboratories. Despite its long history, there is a lack of user-friendly Sanger sequencing data analysis tools that can be run interactively as a web application or at large-scale in batch from the command-line. Results We present Tracy, an efficient and versatile command-line application that enables basecalling, alignment, assembly and deconvolution of sequencing chromatogram files. Its companion web applications make all functionality of Tracy easily accessible using standard web browser technologies and interactive graphical user interfaces. Tracy can be easily integrated in large-scale pipelines and high-throughput settings, and it uses state-of-the-art file formats such as JSON and BCF for reporting chromatogram sequencing results and variant calls. The software is open-source and freely available at https://github.com/gear-genomics/tracy, the companion web applications are hosted at https://www.gear-genomics.com. Conclusions Tracy can be routinely applied in large-scale validation efforts conducted in clinical genomics studies as well as for high-throughput genome editing techniques that require a fast and rapid method to confirm discovered variants or engineered mutations. Molecular biologists benefit from the companion web applications that enable installation-free Sanger chromatogram analyses using intuitive, graphical user interfaces.

The fungal-interactive (fungiphilic) strains BS001, BS007, BS110, and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around Paraburkholderia hospita (containing the species P. terrae, P. hospita, and Paraburkholderia caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T, were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared with the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110, and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T, and strains BS001, BS007, BS110, and BS437), being clearly divergent from the closely related species P. caribensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili, and diverse secretion systems were found.

BACKGROUND: Human respiratory syncytial virus (RSV) is classified into antigenic subgroups A and B. Thirteen genotypes have been defined for RSV-A and 20 for RSV-B, without any consensus on genotype definition. METHODS: We evaluated clustering of RSV sequences published in GenBank until February 2018 to define genotypes by using maximum likelihood and Bayesian phylogenetic analyses and average p-distances. RESULTS: We compared the patterns of sequence clustering of complete genomes; the three surface glycoproteins genes (SH, G, and F, single and concatenated); the ectodomain and the 2nd hypervariable region of G gene. Although complete genome analysis achieved the best resolution, the F, G, and G-ectodomain phylogenies showed similar topologies with statistical support comparable to complete genome. Based on the widespread geographic representation and large number of available G-ectodomain sequences, this region was chosen as the minimum region suitable for RSV genotyping. A genotype was defined as a monophyletic cluster of sequences with high statistical support (≥80% bootstrap and ≥0.8 posterior probability), with an intragenotype p-distance ≤0.03 for both subgroups and an intergenotype p-distance ≥0.09 for RSV-A and ≥0.05 for RSV-B. In this work, the number of genotypes was reduced from 13 to three for RSV-A (GA1-GA3) and from 20 to seven for RSV-B (GB1-GB7). Within these, two additional levels of classification were defined: subgenotypes and lineages. Signature amino acid substitutions to complement this classification were also identified. CONCLUSIONS: We propose an objective protocol for RSV genotyping suitable for adoption as an international standard to support the global expansion of RSV molecular surveillance. ispartof: INFLUENZA AND OTHER RESPIRATORY VIRUSES vol:14 issue:3 pages:274-285 ispartof: location:England status: published

In this study, we aimed to study the effect of fluid shear stress on fibroblasts and BMSCs on plane and groove topographies. The results showed that 0.6-Hz stress had the greatest influence on the alignment, polarity, migration and adhesion of fibroblasts on plane by increasing the expression of reoriented actin and vinculin; whereas 1.0-Hz stress promoted differentiation of fibroblasts into myofibroblasts by increasing Col-I and α-SMA expression. Interestingly, under the given frequency stress, the groove structure strengthened the above characteristics of fibroblasts beyond adhesion, and promoted differentiation of BMSCs into myofibroblasts. The above results indicate that 0.6 Hz may improve the implant-tissue sealing, while 1.0-Hz stress probably causes the disordered fiber deposition around implants.

Purpose There are concerns that malalignment in total knee arthroplasty (TKA) occurs with less experienced surgeons. This study investigates the influence of surgical experience on TKA outcomes. Materials and methods Nineteen patients (38 knees) who underwent bilateral TKA between 2011 and 2015 were included. A supervisor performed knee replacements associated with lower Knee Society Scores (KSS); trainee surgeons operated on the other knee. Knees were categorized into two groups: operations by the supervisor (group S) versus operations by trainee surgeons (group T). Range of motion (ROM), KSS, operative time, hip–knee–ankle angle, and femoral and tibial component angle were evaluated. Results The mean operative time was 92.5 min in group S and 124.2 min in group T (p Conclusions Although operative time was significantly longer for trainee surgeons versus the supervisor, no significant differences in ROM, KSS, or component positioning between supervisor and trainee surgeons were observed. Level of evidence IV (retrospective case series design).

Background Patellofemoral pain (PFP) patients show increased prevalence of patellar malalignment. Structural and alignment abnormalities of the patellofemoral joint (PFJ) may play a role in development of PFP and patellofemoral osteoarthritis (PFOA). Objectives Evaluating associations of patellofemoral alignment and femoral geometry with bony and cartilaginous abnormalities in PFP patients and healthy control subjects. Methods Data from a case-control study were used (64 PFP subjects, 70 control subjects, 57% female, age 23.2 (6.4)). Alignment and femoral geometry measures in the PFJ were determined using MRI. Structural abnormalities in the PFJ associated with OA (bone marrow lesions, osteophytes, minor cartilage defects and Hoffa-synovitis), quantified cartilage composition (T1ρ relaxation times) in the PFJ and perfusion within the patellar bone were examined using different MRI techniques. Associations were analyzed using regression analyses, adjusted for potential confounders. Results Lateral patellar tilt was negatively associated with presence of osteophytes on both patella (OR 0.91; 95% CI 0.84 to 0.98), anterior femur (OR 0.92; 95% CI 0.84 to 0.99) and minor cartilage defects on patella (OR 0.91; 95% CI 0.84 to 0.99). Patella alta was positively associated with the presence of bone marrow lesions in the patella and minor cartilage defects (OR 48.33; 95% CI 4.27 to 547.30 and OR 17.51; 95% CI 1.17 to 262.57, respectively). Patella alta and medial patellar translation were positively associated with T1ρ relaxation times within trochlear cartilage (β 5.2; 95% CI 0.77 to 9.58, and 0.36; 95% CI 0.08 to 0.64, respectively). None of the alignment and geometry measures were associated with bone perfusion. Conclusion Our study implies that associations between patellofemoral alignment and geometry and structural joint abnormalities linked to OA are already present in both PFP patients and healthy control subjects.

Background The relationship between spinal sagittal subtypes and lumbar disc degeneration is unclear. Thus, we aimed to investigate the relationship between lumbar intervertebral disc degeneration and age in asymptomatic healthy individuals with different sagittal alignments. Methods In this cross-sectional observational study, we examined 209 asymptomatic young and middle-aged volunteers (123 women and 86 men) who were divided into the following three groups according to age: groups A (20–30 years), B (31–40 years), and C (41–50 years). The volunteers underwent full-spine standing lateral radiography and magnetic resonance imaging (MRI, 3.0 T) of the lumbar spine. Based on panoramic radiography, two observers measured the spinopelvic parameters and classified the spine into Roussouly subtypes. The degree of disc degeneration was assessed based on T2-weighted images according to the Pfirrmann classification. Results There was a statistically significant difference in the degree of degeneration of type I spine between groups B and C at L4-L5 (P P P P P P P Conclusion The different spinal subtypes have characteristics of lumbar disc degeneration at specific levels with age. We considered that spinal classification could be used as a predictor of lumbar disc degeneration. Our data may be helpful to increase awareness of the relationship between spinal subtypes and lumbar disc degeneration. Level of evidence 3

The aim of this two-centre RCT was to compare pre- and post-operative radiological, clinical and functional outcomes between patient-specific instrumentation (PSI) and conventional instrumented (CI) unicompartmental knee arthroplasty (UKA). It was hypothesised that both alignment methods would have comparable post-operative radiological, clinical and functional outcomes. One hundred and twenty patients were included, and randomly allocated to the PSI or the CI group. Outcome measures were peri-operative outcomes (operation time, length of hospital stay and intra-operative changes of implant size) and post-operative radiological outcomes including the alignment of the tibial and femoral component in the sagittal and frontal plane and the hip–knee–ankle-axis (HKA-axis), rate of adverse events (AEs) and patient-reported outcome measures (PROMs) pre-operatively and at 3, 12 and 24 months post-operatively. There was a statistically significant difference (p

Background Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. Results We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. Conclusion These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.

Long terminal repeat (LTR) retrotransposons are widely distributed across the human genome. They have accumulated through retroviral integration into germline DNA and are latent genetic modules. Active LTR promoters are observed in germline cells; however, little is known about the mechanisms underlying their active transcription in somatic tissues. Here, by integrating our previous transcriptome data set with publicly available data sets, we show that the LTR families MLT2A1 and MLT2A2 are primarily expressed in human four-cell and eight-cell embryos and are also activated in some adult somatic tissues, particularly pineal gland. Three MLT2A elements function as the promoters and first exons of the protein-coding genes ABCE1, COL5A1, and GALNT13 specifically in the pineal gland of humans but not in that of macaques, suggesting that the exaptation of these LTRs as promoters occurred during recent primate evolution. This analysis provides insight into the possible transition from germline insertion to somatic expression of LTR retrotransposons.

This work examines a data-intensive irregular application from genomics that represents a type of Generalized N-Body problems, one of the “seven giants” of the NRC Big Data motifs. In this problem, computations (genome alignments) are performed on sparse data-dependent pairs of inputs, with variable cost computation and variable datum sizes. Unlike simulation-based N-Body problems, there is no inherent locality in the pairwise interactions, and the interaction sparsity depends on particular parameters of the input, which can also affect the quality of the output. We build-on a pre-existing bulk-synchronous implementation, using collective communication in MPI, and implement a new asynchronous one, using cross-node RPCs in UPC++. We establish the intranode comparability and efficiency of both, scaling from one to all core(s) on node. Then we evaluate the multinode scalability from 1 node to 512 nodes (32,768 cores) of NERSC’s Cray XC40 with Intel Xeon Phi “Knight’s Landing” nodes. With real workloads, we examine the load balance of the irregular computation and communication, and the costs of many small asynchronous messages versus few large-aggregated messages, in both latency and overall application memory footprint. While both implementations demonstrate good scaling, the study reveals some of the programming and architectural challenges for scaling this type of data-intensive irregular application, and contributes code that can be used in genomics pipelines or in benchmarking for data analytics more broadly.

Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content, resulting from frequent horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here we introduce Panaroo, a graph based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. We verified our approach through extensive simulations of de novo assemblies using the infinitely many genes model and by analysing a number of publicly available large bacterial genome datasets. Using a highly clonal Mycobacterium tuberculosis dataset as a negative control case, we show that failing to account for annotation errors can lead to pangenome estimates that are dominated by error. We additionally demonstrate the utility of the improved graphical output provided by Panaroo by performing a pan-genome wide association study in Neisseria gonorrhoeae and by analysing gene gain and loss rates across 51 of the major global pneumococcal sequence clusters. Panaroo is freely available under an open source MIT licence at https://github.com/gtonkinhill/panaroo.

Introduction:After a better understanding of normal knee anatomy and physiology, the Kinematic Alignment (KA) technique was introduced to improve clinical outcomes of total knee arthroplasty (TKA). The goal of the KA technique is to restore the pre-arthritic constitutional lower limb alignment of the patient. There is, however, a large range of normal knee anatomy. Unusual anatomies may be biomechanically inferior and affect TKA biomechanics and wear patterns. In 2011, the leading author proposed the restricted kinematic alignment (rKA) protocol, setting boundaries to KA for patients with an outlier or atypical knee anatomy.Material and Equipment:rKA aims to reproduce the constitutional knee anatomy of the patient within a safe range. Its fundamentals are based on sound comprehension of lower limb anatomy variation. There are five principles describing rKA: (1) Combined lower limb coronal orientation should be ± 3° of neutral; (2) Joint line orientation coronal alignment should be within ± 5° of neutral; (3) Natural knee's soft tissues tension/ laxities should be preserved/restored; (4) Femoral anatomy preservation is prioritized; (5) The unloaded/most intact knee compartment should be resurfaced and used as the pivot point when anatomical adjustment is required. An algorithm was developed to facilitate the decision-making.Methods:Since ~50% of patients will require anatomic modification to fit within rKA boundaries, rKA is ideally performed with patient-specific instrumentation (PSI), intra-operative computer navigation or robotic assistance. rKA surgical technique is presented in a stepwise manner, following the five principles in the algorithm.Results:rKA produced excellent mid-term clinical results in cemented or cementless TKA. Gait analysis showed that rKA TKA patients had gait patterns that were very close to a non-operated control group, and these kinematics differences translated into significantly better postoperative patient-reported scores than mechanical alignment (MA) TKA cases.Discussion:Aiming to improve the results of MA TKA, rKA protocol offers a satisfactory compromise that recreates patients' anatomy in most cases, omitting the need for extensive corrections and soft tissue releases that are often required with MA. Moreover, it precludes the reproduction of extreme anatomies seen with KA.

Whole-genome sequencing (WGS) is becoming the de facto standard for bacterial typing and outbreak surveillance of resistant bacterial pathogens. However, interoperability for WGS of bacterial outbreaks is poorly understood. We hypothesized that harmonization of WGS for outbreak surveillance is achievable through the use of identical protocols for both data generation and data analysis. A set of 30 bacterial isolates, comprising of various species belonging to the Enterobacteriaceae family and Enterococcus genera, were selected and sequenced using the same protocol on the Illumina MiSeq platform in each individual centre. All generated sequencing data were analysed by one centre using BioNumerics (6.7.3) for (i) genotyping origin of replications and antimicrobial resistance genes, (ii) core-genome multi-locus sequence typing (cgMLST) for Escherichia coli and Klebsiella pneumoniae and whole-genome multi-locus sequencing typing (wgMLST) for all species. Additionally, a split k-mer analysis was performed to determine the number of SNPs between samples. A precision of 99.0% and an accuracy of 99.2% was achieved for genotyping. Based on cgMLST, a discrepant allele was called only in 2/27 and 3/15 comparisons between two genomes, for E. coli and K. pneumoniae, respectively. Based on wgMLST, the number of discrepant alleles ranged from 0 to 7 (average 1.6). For SNPs, this ranged from 0 to 11 SNPs (average 3.4). Furthermore, we demonstrate that using different de novo assemblers to analyse the same dataset introduces up to 150 SNPs, which surpasses most thresholds for bacterial outbreaks. This shows the importance of harmonization of data-processing surveillance of bacterial outbreaks. In summary, multi-centre WGS for bacterial surveillance is achievable, but only if protocols are harmonized.

Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in December 2019 in Wuhan, China. It was quickly established that both the symptoms and the disease severity may vary from one case to another and several strains of SARS-CoV-2 have been identified. To gain a better understanding of the wide variety of SARS-CoV-2 strains and their associated symptoms, thousands of SARS-CoV-2 genomes have been sequenced in dozens of countries. In this article, we introduce COVIDomic, a multi-omics online platform designed to facilitate the analysis and interpretation of the large amount of health data collected from patients with COVID-19. The COVIDomic platform provides a comprehensive set of bioinformatic tools for the multi-modal metatranscriptomic data analysis of COVID-19 patients to determine the origin of the coronavirus strain and the expected severity of the disease. An integrative analytical workflow, which includes microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification, allows to analyze the presence of the most common microbial organisms, their antibiotic resistance, the severity of the infection and the set of the most probable geographical locations from which the studied strain could have originated. The online platform integrates a user friendly interface which allows easy visualization of the results. We envision this tool will not only have immediate implications for management of the ongoing COVID-19 pandemic, but will also improve our readiness to respond to other infectious outbreaks., Author summary This article introduces COVIDomic, a new integrative multi-omics online platform designed to facilitate the analysis of the large amount of health data collected from COVID-19 patients. The COVIDomic platform includes a user-friendly interface and provides a set of bioinformatics tools for the analysis of multi-modal metatranscriptomic data to determine the origin of the coronavirus strain and the expected severity of the disease. An analytical workflow includes microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification. These features allow studying the presence of common microbial organisms, their antibiotic resistance and the severity of the infection, as well as obtaining insights on the geographical locations from which the strain could have originated. Such openly distributed multi-modal platform will greatly accelerate the ongoing COVID-19 research and improve our readiness to respond to other infectious outbreaks.

International audience; The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676x sequencing depth) from PacBio and Illumina short-reads, in combination with 10x Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.