•Mass spectral databases play a key role in metabolomics.•Advantages and limitations of public and commercial databases are underlined.•The overlap of compounds in public and commercial databases is ...calculated.•Future prospects of mass spectral databases are discussed.
At present, mass spectrometry (MS)-based metabolomics has been widely used to obtain new insights into human, plant, and microbial biochemistry; drug and biomarker discovery; nutrition research; and food control. Despite the high research interest, identifying and characterizing the structure of metabolites has become a major drawback for converting raw MS data into biological knowledge. Comprehensive and well-annotated MS-based spectral databases play a key role in serving this purpose via the formation of metabolite annotations. The main characteristics of the mass spectral databases currently used in MS-based metabolomics are reviewed in this study, underlining their advantages and limitations. In addition, the overlap of compounds with MSn (n ≥ 2) spectra from authentic chemical standards in most public and commercial databases has been calculated for the first time. Finally, future prospects of mass spectral databases are discussed in terms of the needs posed by novel applications and instrumental advancements.
Purpose To report outcomes after a minimum of 5 years following pyrocarbon interposition (PyroDisk) trapeziometacarpal joint implant for osteoarthritis at a single center. Methods We retrospectively ...reviewed the midterm clinical and radiological outcomes of 19 patients who had a pyrocarbon interposition implant (PyroDisk; Integra Life Sciences, Plainsboro, NJ) arthroplasty. The rate and causes of repeat surgeries, revisions, and complications were examined. Results The mean follow-up period was 68 months. Patient satisfaction was high. The mobility of the operated thumb was restored to a range of motion comparable with that of the contralateral thumb. Grip strength improved by 26%. Overall function, according to the Quick Disabilities of the Arm, Shoulder, and Hand score, showed an average improvement of 71 to 20. Pain decreased by 78% according to the numerical rating scale. Radiological evaluation using a modification of the system described by Herren revealed progression of the periprosthetic lucency (grade I–II) of the implant after 5 years in 5 of 19 (26%) patients. Progression of lucency did not predict implant loosening or failure at 5 years. Two patients had symptomatic instability that required revision. No dislocations occurred. The 5-year survival of the prosthesis was 90%. Conclusions The PyroDisk implant for treating advanced trapeziometacarpal arthritis did not demonstrate superiority over published outcome data of trapeziectomy with or without ligament reconstruction and tendon interposition. Type of study/level of evidence Therapeutic IV.
Background:
Intra-articular injections of platelet-rich plasma (PRP) to treat symptoms of knee osteoarthritis (OA) have been successfully used in young patients and in the early stages of disease. No ...previous studies have analyzed outcomes of PRP injections during the late stages.
Hypothesis:
PRP reduces pain and leads to a more effective and lasting functional recovery than corticosteroid with local anesthetic.
Study Design:
Randomized controlled trial; Level of evidence, 2.
Methods:
A total of 75 patients with symptomatic knee OA (Kellgren-Lawrence grade 3 to 4) were enrolled in this study between August 2013 and July 2014. Patients were randomized to treatment either with a single leukocyte-reduced PRP or corticosteroid intra-articular injection. The primary variable was visual analog scale assessment at 1 month. Secondary outcomes were the Knee injury and Osteoarthritis Outcome Score (KOOS) and Short Form–36 (SF-36) at 1, 3, and 6 months after treatment. Patient satisfaction at final follow-up was assessed. Both groups were homogeneous and comparable in baseline characteristics.
Results:
All variables improved in both groups. Statistical differences between groups were not found for the majority of the outcome variables, although the magnitude of improvements tended to be greater in the PRP group. Quality-of-life differences between values at 3 and 6 months versus baseline increased significantly more in the study group (P = .05 and .03, respectively), and so did general health perception differences at 6 months (P = .018).
Conclusion:
A single PRP intra-articular injection is effective for relieving pain and improving activities of daily living and quality of life in late-stage knee OA. For patients with late-stage knee OA who are 67 years or older, 1 intra-articular injection of PRP has similar results to 1 shot of corticosteroid.
Metabolomics is a relatively new "omics" approach used to characterize metabolites in a biological system at baseline and following a diversity of stimuli. However, the metabolomic response to ...exercise in hypoxia currently remains unknown. To examine this, 24 male participants completed 1 h of exercise at a workload corresponding to 75% of pre-determined O
in hypoxia (F
o
= 0.16%), and repeated in normoxia (F
o
= 0.21%), while pre- and post-exercise and 3 h post-exercise metabolites were analyzed using a LC ESI-qTOF-MS untargeted metabolomics approach in serum samples. Exercise in hypoxia and in normoxia independently increased metabolism as shown by a change in a combination of twenty-two metabolites associated with lipid metabolism (
< 0.05, pre vs. post-exercise), though hypoxia
did not induce a greater metabolic change when compared with normoxia (
> 0.05). Recovery from exercise in hypoxia independently decreased seventeen metabolites associated with lipid metabolism (
< 0.05, post vs. 3 h post-exercise), compared with twenty-two metabolites in normoxia (
< 0.05, post vs. 3 h post-exercise). Twenty-six metabolites were identified as responders to exercise and recovery (pooled hypoxia and normoxia pre vs. recovery,
< 0.05), including metabolites associated with purine metabolism (adenine, adenosine and hypoxanthine), the amino acid phenylalanine, and several acylcarnitine molecules. Our novel data provides preliminary evidence of subtle metabolic differences to exercise and recovery in hypoxia and normoxia. Specifically, exercise in hypoxia activates metabolic pathways aligned to purine and lipid metabolism, but this effect is not selectively different from exercise in normoxia. We also show that exercise
can activate pathways associated with lipid, protein and purine nucleotide metabolism.
Several metabolomic software programs provide methods for peak picking, retention time alignment and quantification of metabolite features in LC/MS-based metabolomics. Statistical analysis, however, ...is needed in order to discover those features significantly altered between samples. By comparing the retention time and MS/MS data of a model compound to that from the altered feature of interest in the research sample, metabolites can be then unequivocally identified. This paper reports on a comprehensive overview of a workflow for statistical analysis to rank relevant metabolite features that will be selected for further MS/MS experiments. We focus on univariate data analysis applied in parallel on all detected features. Characteristics and challenges of this analysis are discussed and illustrated using four different real LC/MS untargeted metabolomic datasets. We demonstrate the influence of considering or violating mathematical assumptions on which univariate statistical test rely, using high-dimensional LC/MS datasets. Issues in data analysis such as determination of sample size, analytical variation, assumption of normality and homocedasticity, or correction for multiple testing are discussed and illustrated in the context of our four untargeted LC/MS working examples.
ABSTRACT Introduction Necrotising fasciitis (NF) is potentially life-threatening soft-tissue infection. Early diagnosis and aggressive surgical debridement are critical to decrease mortality and ...morbidity. The impacts of new management technologies such as hydro-bisturi-assisted debridement (HAD) and negative pressure wound therapy (NPWT) are not yet clear with respect to treatment of NF. The objective of this study was to describe laboratory (including LRINEC score), clinical and microbiological factors, treatment methods and outcomes related to managing necrotising fasciitis, focusing on the implementation of new treatment methods in our centre. Methods From June 2010 to June 2014, adult patients diagnosed with necrotising fasciitis affecting an upper or lower limb that were admitted to our hospital, a referral tertiary care centre, were eligible to participate in this study. Demographic data, clinical features, location of infection, Laboratory Risk Indicator for Necrotising Fasciitis (LRINEC) score on the day of admission, microbiology and laboratory results, use of HAD, wound management using NPWT, and patient outcomes were retrospectively analysed. A univariate risk factor analysis was performed, in an attempt to define prognostic factors for mortality. Results A total of 20 patients satisfied the inclusion criteria. Type II NF (Group A ß-haemolytic streptococci) was found in 8 cases (40%). The average LRINEC score on the day of admission was 6. The lower extremity was affected in 60% of the cases. All patients were treated operatively, with 2.5 interventions on average. Hydro-bisturi was used in the first debridement in 40% of the cases (8 out 20). In 75% of the studied cases, Negative Pressure Wound Therapy (NPWT) was the technique selected for surgical wound management. The global mortality rate was 30%. On univariate analysis, the only factors significantly associated with mortality were high levels of creatinin ( p = 0.033) and low blood glucose levels ( p = 0.012). Finally, four amputations were observed in this series. Conclusion We confirm that necrotising fasciitis (NF) of the extremities, despite new advancements in treatment and critical care management, is still a potentially life-threatening soft-tissue infection (30% mortality). New, advanced wound management modalities have been heavily used in management of necrotising fasciitis, but these have not had significant impacts on morbidity and mortality rates.
The microbial production of fine chemicals provides a promising biosustainable manufacturing solution that has led to the successful production of a growing catalog of natural products and high-value ...chemicals. However, development at industrial levels has been hindered by the large resource investments required. Here we present an integrated Design-Build-Test-Learn (DBTL) pipeline for the discovery and optimization of biosynthetic pathways, which is designed to be compound agnostic and automated throughout. We initially applied the pipeline for the production of the flavonoid (2
)-pinocembrin in
, to demonstrate rapid iterative DBTL cycling with automation at every stage. In this case, application of two DBTL cycles successfully established a production pathway improved by 500-fold, with competitive titers up to 88 mg L
. The further application of the pipeline to optimize an alkaloids pathway demonstrates how it could facilitate the rapid optimization of microbial strains for production of any chemical compound of interest.
Because of the wide range of chemically and structurally diverse metabolites, efforts to survey the complete metabolome rely on the implementation of multiplatform approaches based on nuclear ...magnetic resonance (NMR) and mass spectrometry (MS). Sample preparation disparities between NMR and MS, however, may limit the analysis of the same samples by both platforms. Specifically, deuterated solvents used in NMR strategies can complicate LC/MS analysis as a result of potential mass shifts, whereas acidic solutions typically used in LC/MS methods to enhance ionization of metabolites can severely affect reproducibility of NMR measurements. These intrinsically different sample preparation requirements result in the application of different procedures for metabolite extraction, which involve additional sample and unwanted variability. To address this issue, we investigated 12 extraction protocols in liver tissue involving different aqueous/organic solvents and temperatures that may satisfy the requirements for both NMR and LC/MS simultaneously. We found that deuterium exchange did not affect LC/MS results, enabling the measurement of metabolites by NMR and, subsequently, the direct analysis of the same samples by using LC/MS with no need for solvent exchange. Moreover, our results show that the choice of solvents rather than the temperature determined the extraction efficiencies of metabolites, a combination of methanol/chloroform/water and methanol/water being the extraction methods that best complement NMR and LC/MS analysis for metabolomic studies.
Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the ...usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.
Background
Most athletes who undergo revision of the anterior cruciate ligament reconstruction (ACLR) aim to return to their preinjury sport at a similar level of performance while minimizing the ...risk for reinjury. Additional lateral extra-articular tenodesis (LET) has recently been correlated with improved outcomes and low complication rate. Yet, there are few series evaluating return-to-sport (RTS) and clinical outcomes after revision ACLR using bone-patellar tendon-bone (BPTB) and LET in athletes.
Methods
The study cohort consisted of 19 eligible athletes who had undergone their first revision ACLR using BPTB and LET (modified Lemaire) between January 2019 and 2020. Patients were prospectively followed and interviewed in a sports activity survey during a 2-year follow-up.
Results
Despite all patients returning to sports after revision ACLR surgery, 52.6% resumed playing at their preinjury level. Furthermore, patient-reported functional outcomes improved significantly following revision surgery, as evidenced by improvements in IKDC 64.4 (± 12) to 87.8 (± 6), Lysholm 71.27 (± 12) to 84.2 (± 9.7), and SF-12 scales Physical: 53.3 (± 3) 57 (± 1.2); Mental: 50.2 (± 3.3) to 52.7 (± 2.4). One case (5.3%) experienced persistent pain and underwent reoperation for a partial meniscectomy.
Conclusion
After revision ACLR using autologous BPTB and LET, all active individuals are expected to RTS, similar to primary ACLR. The difference comes down to returning to the preinjury level, where the levels are lower depending on the sport and initial level of play. Good mid-term functional outcomes with a low complication rate can be expected in most cases.
Study design
Case series; Level of evidence IV.
Ethical Committee Approval Number
PR(ATR)79/2021 and HCB/2023/0173.
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