Adult tissue repair and regeneration require stem-progenitor cells that can self-renew and generate differentiated progeny. Skeletal muscle regenerative capacity relies on muscle satellite cells ...(MuSCs) and their interplay with different cell types within the niche. However, our understanding of skeletal muscle tissue cellular composition is limited. Here, using a combined approach of single-cell RNA sequencing and mass cytometry, we precisely mapped 10 different mononuclear cell types in adult mouse muscle. We also characterized gene signatures and determined key discriminating markers of each cell type. We identified two previously understudied cell populations in the interstitial compartment. One expresses the transcription factor scleraxis and generated tenocytes in vitro. The second expresses markers of smooth muscle and mesenchymal cells (SMMCs) and, while distinct from MuSCs, exhibited myogenic potential and promoted MuSC engraftment following transplantation. The blueprint presented here yields crucial insights into muscle-resident cell-type identities and can be exploited to study muscle diseases.
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•Combination of single-cell RNA sequencing and mass cytometry•Construction of a cell atlas of adult skeletal muscle•Skeletal muscle is composed of 10 mononucleated cell types and myofibers•Skeletal muscle contains interstitial tenocytes and smooth muscle-mesenchymal cells
A strong characterization of cell types present in adult skeletal muscle is needed. Giordani et al. use both single-cell transcriptomics and mass cytometry to build a single-cell survey of adult skeletal muscle tissue and reveal understudied cell populations.
The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is ...caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.
The growth of next-generation sequencing means that more effective and efficient archiving methods are needed to store the generated data for public dissemination and in anticipation of more mature ...analytical methods later. This article examines methods for compressing the quality score component of the data to partly address this problem.
We compare several compression policies for quality scores, in terms of both compression effectiveness and overall efficiency. The policies employ lossy and lossless transformations with one of several coding schemes. Experiments show that both lossy and lossless transformations are useful, and that simple coding methods, which consume less computing resources, are highly competitive, especially when random access to reads is needed.
Our C++ implementation, released under the Lesser General Public License, is available for download at http://www.cb.k.u-tokyo.ac.jp/asailab/members/rwan.
Supplementary data are available at Bioinformatics online.
Abstract
Background
Many patients experience bilateral knee osteoarthritis and require bilateral total knee replacement (TKR). Same-stage, bilateral TKR is proposed to be a cost-effective and safe ...solution compared to two-stage, but conflicting results in the literature are reported. We aim to compare the costs, safety, and rehabilitation performance of patients in same-stage versus two-stage, bilateral TKR with our centre’s perioperative protocol.
Materials and methods
We retrospectively reviewed 175 patients (95 same-stage, 80 two-stage) who had undergone bilateral TKR in our centre. Patient selection for same-stage, bilateral TKR was strictly protocol-driven and required fulfilment of all criteria, including age < 75 years, American Society of Anesthesiologists (ASA) grade 1 or 2, body mass index (BMI) < 40, and having non-complex arthritis. All patients followed a standardised pre-operative, intra-operative, and post-operative Enhanced Recovery After Surgery (ERAS) protocol. The cost, safety profiles, and rehabilitation outcomes were compared between the same-stage and two-stage groups.
Results
The same-stage, bilateral TKR reduced the length of hospital stays by 5.71 days per patient, decreased the operation time by 27.4 min, saved 3.34 (18.6%) physiotherapy sessions, and 3.78 (51.5%) occupational therapy sessions. The same-stage group experienced a higher haemoglobin drop but no significant difference in transfusion percentage, transfusion volume, complication rate, and readmission rate. The two-stage subgroup with anaesthetic risk, age, and BMI similar to the same-stage group showed the same results. Same-stage, bilateral TKR patients experienced no significant difference in final post-operative pain levels and rehabilitation outcomes as two-stage TKR patients.
Conclusion
This study showed that same-stage, bilateral TKR can reduce costs, with similar safety profiles and rehabilitation outcomes compared to the two-stage, bilateral TKR.
Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and ...expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral-human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate.
VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq
The use of fluoroscopy is widespread within different medical specialties. Improper protection may cause significant radiation hazard to medical personnel. To evaluate the concepts on radiation ...safety and fluoroscopy use among orthopaedic surgeons and to reflect our current training on this issue, a survey was distributed to perform an audit in our department, an academic unit. Twenty-eight orthopaedic surgeons replied. Amongst our participants, 96.4% used a lead apron at all times. Only 33% used a thyroid shield, 67% never used radiation goggles and 96% never used radiation protection gloves. 53.6% and 46.4% of participants position the fluoroscopy incorrectly in the anteroposterior and lateral positions, respectively, during use. There is clearly a need for improved safety amongst orthopaedic surgeons. A literature review was further performed, showing the hazards of fluoroscopy for doctors, including the risk of cataracts, radiation dermatitis, skin cancer and thyroid cancer. Hazards specific to females, including breast cancer risk, and in-utero irradiation of foetus were also thoroughly discussed. Recommendations towards radiation safety and practical measures to reduce fluoroscopy radiation hazard during procedure were made. Education and training to doctors on this invisible hazard is strongly advised.
Although skeletal muscle cells can be generated from human induced pluripotent stem cells (iPSCs), transgene-free protocols include only limited options for their purification and expansion. In this ...study, we found that fluorescence-activated cell sorting-purified myogenic progenitors generated from healthy controls and Pompe disease iPSCs can be robustly expanded as much as 5 × 1011-fold. At all steps during expansion, cells could be cryopreserved or differentiated into myotubes with a high fusion index. In vitro, cells were amenable to maturation into striated and contractile myofibers. Insertion of acid α-glucosidase cDNA into the AAVS1 locus in iPSCs using CRISPR/Cas9 prevented glycogen accumulation in myotubes generated from a patient with classic infantile Pompe disease. In vivo, the expression of human-specific nuclear and sarcolemmar antigens indicated that myogenic progenitors engraft into murine muscle to form human myofibers. This protocol is useful for modeling of skeletal muscle disorders and for using patient-derived, gene-corrected cells to develop cell-based strategies.
•Transgene-free protocol for generation and expansion of myogenic progenitors•Differentiation into contractile skeletal muscle cells in vitro•Correction of glycogen accumulation in Pompe disease using CRISPR/cas9•Contribution to muscle regeneration in vivo
Van der Wal et al. present a robust protocol for the transgene-free generation and purification of myogenic progenitors from human iPSCs and for their expansion up to 5 × 1011-fold. After gene editing in vitro, these myogenic progenitors matured into contractile skeletal muscle cells, reversing Pompe disease pathology. In vivo, myogenic progenitors contributed to muscle regeneration.
Cellulomonas biazotea
, a Gram-positive cellulolytic bacterium isolated from soil, is capable of producing a complete cellulase complex exhibiting endoglucanase, exoglucanase, and cellobiase ...activities. Despite the presence of a full complement of all three types of cellulases, samples prepared from both cell lysates and culture media of
C. biazotea
showed only weak synergistic activities formed among the cellulase components, as reflected by their inefficient performance in filter paper hydrolysis. However, when the five previously characterized recombinant cellobiases of
C. biazotea
were mixed individually or in different combinations with recombinant enzyme preparations (CenA/Cex) containing an endoglucanase, CenA, and an exoglucanase, Cex, of another
Cellulomonas
species,
C. fimi
, the cellulase cocktails exhibited not only much higher but also synergistic activities in filter paper hydrolysis. Among the 5
C. biazotea
cellobiases studied, Cba2 was shown to perform 2.8 to 3.8 times better than other homologous isozymes when acting individually with CenA/Cex. More noteworthy is that when Cba2 and Cba4 were added together to the reaction mixture, an even better synergistic effect was achieved. The filter paper activities resulting from Cba2 and Cba4 interacting with CenA/Cex are comparable to those obtained from some commercial fungal cellulase mixtures. To our knowledge, our results represent the first demonstration of synergistic effects on filter paper hydrolysis achieved using recombinant bacterial cellulases.
Total wrist replacement (TWR) is rarely done in the Asia-Pacific region. The aim of this study is to report the surgical outcomes and experience of TWR in patients with advanced arthritis.
This is a ...retrospective review of all TWR patients in the Department of Orthopaedics and Traumatology, Prince of Wales Hospital, Hong Kong, which is a university tertiary centre, from January 2004 to March 2023. Recorded demographic parameters include gender, age upon surgery, pathology, types of implants and follow-up period. The surgical outcome parameters include range of motion, grip strength, wrist function assessment, radiological and clinical complications and any related secondary operations. Postoperative X-ray and clinical notes were reviewed. All wrist function assessments were performed by specialised occupational therapists according to protocol.
The study included a total of 12 wrists of 10 patients, all Chinese-Asian, with a mean age of 61.4 years at surgery. Larsen grade V arthritis constituted 50% and grade IV 16.7% of the patients, amongst which 33% had volar subluxation. The mean follow-up period was 97.4 months (21-205 months). The mean grip strength was 64.2% of the unaffected side. The mean postoperative Disabilities of Arm, Shoulder and Hand (DASH) score was 41.12% and patient-rated wrist/hand evaluation (PRWE) score 18.0. Complication incidence was 16.67% for loosening, 8.3% for metallosis and 8.3% for infection. One patient required conversion to total wrist arthrodesis due to metallosis. No patient suffered from dislocation, periprosthetic fracture and infection.
TWR is an effective and safe alternative to total wrist arthrodesis with comparable outcomes. Our series outcomes are satisfactory and in line with literature. With meticulous soft tissue release and balancing, volar subluxation can also be corrected and may not be a contraindication.
Level IV (Therapeutic).
IntroductionWe designed and implemented a patient-centered, data-driven, holistic care model with evaluation of its impacts on clinical outcomes in patients with young-onset type 2 diabetes (T2D) for ...which there is a lack of evidence-based practice guidelines.Research design and methodsIn this 3-year Precision Medicine to Redefine Insulin Secretion and Monogenic Diabetes-Randomized Controlled Trial, we evaluate the effects of a multicomponent care model integrating use of information and communication technology (Joint Asia Diabetes Evaluation (JADE) platform), biogenetic markers and patient-reported outcome measures in patients with T2D diagnosed at ≤40 years of age and aged ≤50 years. The JADE-PRISM group received 1 year of specialist-led team-based management using treatment algorithms guided by biogenetic markers (genome-wide single-nucleotide polymorphism arrays, exome-sequencing of 34 monogenic diabetes genes, C-peptide, autoantibodies) to achieve multiple treatment goals (glycated hemoglobin (HbA1c) <6.2%, blood pressure <120/75 mm Hg, low-density lipoprotein-cholesterol <1.2 mmol/L, waist circumference <80 cm (women) or <85 cm (men)) in a diabetes center setting versus usual care (JADE-only). The primary outcome is incidence of all diabetes-related complications.ResultsIn 2020–2021, 884 patients (56.6% men, median (IQR) diabetes duration: 7 (3–12) years, current/ex-smokers: 32.5%, body mass index: 28.40±5.77 kg/m2, HbA1c: 7.52%±1.66%, insulin-treated: 27.7%) were assigned to JADE-only (n=443) or JADE-PRISM group (n=441). The profiles of the whole group included positive family history (74.7%), general obesity (51.4%), central obesity (79.2%), hypertension (66.7%), dyslipidemia (76.4%), albuminuria (35.4%), estimated glomerular filtration rate <60 mL/min/1.73 m2 (4.0%), retinopathy (13.8%), atherosclerotic cardiovascular disease (5.2%), cancer (3.1%), emotional distress (26%–38%) and suboptimal adherence (54%) with 5-item EuroQol for Quality of Life index of 0.88 (0.87–0.96). Overall, 13.7% attained ≥3 metabolic targets defined in secondary outcomes. In the JADE-PRISM group, 4.5% had pathogenic/likely pathogenic variants of monogenic diabetes genes; 5% had autoantibodies and 8.4% had fasting C-peptide <0.2 nmol/L. Other significant events included low/large birth weight (33.4%), childhood obesity (50.7%), mental illness (10.3%) and previous suicide attempts (3.6%). Among the women, 17.3% had polycystic ovary syndrome, 44.8% required insulin treatment during pregnancy and 17.3% experienced adverse pregnancy outcomes.ConclusionsYoung-onset diabetes is characterized by complex etiologies with comorbidities including mental illness and lifecourse events.Trial registration numberNCT04049149.
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