Labelled dataset for Ultra-Low Temperature Freezer to aid dynamic modelling & fault detection and diagnostics.

Ultra-low temperature (ULT) freezers are used to store perishable biological contents and are among the most energy-intensive equipment in laboratory buildings, biobanks, and similar settings. To ensure reliable and efficient operation, it is essential to implement data-driven fault detection and diagnostic algorithms, along with energy optimization techniques. This study presents labelled and long-term ULT-freezer performance dataset, the first of its kind, derived from 53 ULT freezers featuring two different control strategies. The dataset comprises high-resolution historical operation data spanning up to 10 years. More than 10 attributes are recorded from the freezing chamber and critical locations in the refrigeration systems. The dataset is labelled with regular events, such as door openings, as well as fault events obtained from 46 service reports. A scalable data pipeline, consisting of extraction, transformation, and loading processes, is developed to convert the raw data into a format ready for analysis. The dataset can be utilized to support the development of data-driven models and algorithms that advance the intelligent digital operation of ULT freezers.

A synthetic data set to benchmark anti-money laundering methods.

Bank transactions are highly confidential. As a result, there are no real public data sets that can be used to investigate and compare anti-money laundering (AML) methods in banks. This severely limits research on important AML problems such as efficiency, effectiveness, class imbalance, concept drift, and interpretability. To address the issue, we present SynthAML: a synthetic data set to benchmark statistical and machine learning methods for AML. The data set builds on real data from Spar Nord, a systemically important Danish bank, and contains 20,000 AML alerts and over 16 million transactions. Experimental results indicate that performance on SynthAML can be transferred to the real world. As use cases, we present and discuss open problems in the AML literature.

Fluorescence-activated cell sorting and phenotypic characterization of human fibro-adipogenic progenitors.

The ability of stem cells to activate and differentiate is critical for maintaining the regenerative capacity of skeletal muscle. Here, we detail steps for specific quantification and isolation of primary human fibro-adipogenic progenitors and skeletal muscle stem cells using fluorescence-activated cell sorting. We describe important phenotypic traits such as time to enter the cell cycle and assessment of cell differentiation for the isolated cell populations. The technique has been applied on tissue obtained from surgery and needle biopsies. For complete details on the use and execution of this protocol, please refer to Farup et al. (2021).1.

Systematic evaluation of isolation processes of microorganisms using spatial statistics.

The evaluation of inoculation processes of microorganisms by robotic systems as well as by lab-technicians is compensable and can be missing consistency as human judgment will depend on the individual and may therefore be biased and less effective than models and algorithms evaluating spatial patterns. To address this problem, nearest neighbor analysis was used to investigate if it could be utilized as a method to evaluate isolation processes. The nearest neighbor analysis results in a comparable numeric value on the isolation process, which can be used to assess results of different inoculation processes. In this article, images of Petri dishes and simulated plates are used to investigate the effectiveness of nearest neighbor analysis, which is a method within spatial statistics. This analysis is applied to spatial data created by applying computer vision to localize the colonies on the plates. When evaluating plates made with the streaking technique method, it was found to be ineffective as the dense parts of the distribution resulted in the computer vision being unable to locate all of the colonies. Therefore, the nearest neighbor analysis is not suitable to evaluate streaking plates and other methods to evaluate such plates should be developed. However, when evaluating Petri dishes where the spread plating technique had been applied, it was found that nearest neighbor analysis can be a useful way to systematically evaluate isolation processes.

A randomized placebo-controlled trial of nicotinamide riboside and pterostilbene supplementation in experimental muscle injury in elderly individuals.

BACKGROUNDDuring aging, there is a functional decline in the pool of muscle stem cells (MuSCs) that influences the functional and regenerative capacity of skeletal muscle. Preclinical evidence has suggested that nicotinamide riboside (NR) and pterostilbene (PT) can improve muscle regeneration, e.g., by increasing MuSC function. The objective of this study was to investigate if supplementation with NR and PT (NRPT) promotes skeletal muscle regeneration after muscle injury in elderly individuals by improved recruitment of MuSCs.METHODSThirty-two elderly individuals (55-80 years of age) were randomized to daily supplementation with either NRPT (1,000 mg NR and 200 mg PT) or matched placebo. Two weeks after initiation of supplementation, skeletal muscle injury was induced by electrically induced eccentric muscle work. Skeletal muscle biopsies were obtained before, 2 hours after, and 2, 8, and 30 days after injury.RESULTSA substantial skeletal muscle injury was induced by the protocol and associated with release of myoglobin and creatine kinase, muscle soreness, tissue edema, and a decrease in muscle strength. MuSC content, proliferation, and cell size revealed a large demand for recruitment after injury, but this was not affected by NRPT. Furthermore, histological analyses of muscle fiber area, central nuclei, and embryonic myosin heavy chain showed no NRPT supplementation effect.CONCLUSIONDaily supplementation with 1,000 mg NR and 200 mg PT is safe but does not improve recruitment of the MuSC pool or other measures of muscle recovery in response to injury or subsequent regeneration in elderly individuals.TRIAL REGISTRATIONClinicalTrials.gov NCT03754842.FUNDINGNovo Nordisk Foundation (NNF17OC0027242) and Novo Nordisk Foundation CBMR.

Four of five frequently used orthopedic PROMs possess inadequate content validity: a COSMIN evaluation of the mHHS, HAGOS, IKDC-SKF, KOOS and KNEES-ACL.

PURPOSE: Content validity is the most important property of PROMs. The COSMIN initiative has published guidelines for evaluating the content validity of PROMs, but they have only sparsely been applied to relevant PROMs for musculoskeletal conditions. The aim of this study was to use the COSMIN Risk of Bias checklist to evaluate the content validity of five PROMs, that are highly relevant in musculoskeletal research and used by the arthroscopic surgery community: the modified Harris' Hip Score (mHHS), the Copenhagen Hip and Groin Outcome Score (HAGOS), the International Knee Documentation Committee Subjective Knee evaluation Form (IKDC-SKF), the Knee injury and Osteoarthritis Outcome Score (KOOS) and the Knee Numeric-Entity Evaluation Score ACL (KNEES-ACL). METHODS: The development articles for the five PROMs were identified through searches in PubMed and SCOPUS. A literature search was performed to identify additional studies assessing content validity of the PROMs. Additional information, necessary for the assessments, was obtained from the PROM developers after direct request. To evaluate the quality of the development studies and rate the content validity, the COSMIN Risk of Bias checklist was applied to all studies. RESULTS: All five development studies were identified. Three subsequent content validity studies were identified, all evaluating KOOS and one also IKDC. One content validity study was of inadequate quality and excluded from further analysis. The development of mHHS, IKDC-SKF, and KOOS was rated inadequate and possess insufficient content validity for their target populations. Due to the irrelevance of multiple items, KOOS was in particular inappropriate to evaluate patients with an ACL injury. The development of HAGOS was also rated inadequate, although the insufficiency aspects can be regarded as minor. KNEES-ACL possessed sufficient content validity. CONCLUSION: Out of five PROMs, only KNEES-ACL possessed sufficient content validity. Particularly, KOOS should not be used as an outcome for patients with an ACL injury. There is an urgent need for condition-specific PROMs for musculoskeletal conditions, developed with adequate methods. LEVEL OF EVIDENCE: III.

Longer retrieval distances to the automated external defibrillator reduces survival after out-of-hospital cardiac arrest.

AIMS: To evaluate and compare survival after out-of-hospital (OHCA), where an automated external defibrillator (AED) was used, in densely, moderately and thinly populated areas. Also, to evaluate the association between AED retrieval distance and survival after OHCA. METHODS: From 2014 to 2018, AEDs used during OHCA in the region of Southern Denmark were systematically collected. OHCAs were included if the OHCA address was known. OHCAs at nursing homes were excluded. To evaluate population density, a map with 1000 × 1000 meter grid cells was used with each cell color-graded according to the number of inhabitants. Densely, moderately and thinly populated areas were defined as ≥200 inhabitants, 20-199 inhabitants and 0-19 inhabitants per km2, respectively. Primary outcome was 30-day survival. RESULTS: A total of 423 cases of OHCA were included, of which 207 (49%) occurred in densely populated areas, while 78 (18%) and 138 (33%) occurred in moderately and thinly populated areas, respectively. AED retrieval distances were: densely populated 105 m (IQR 5-450), moderately populated 220 m (IQR 5-450) and thinly populated 350 m (IQR 5-1500) (P < 0.001). Thirty-day survival was 40%, 31% and 34%, respectively (P = 0.3). In a multivariable regression analysis, mortality increased with 10% per 100 m an AED was placed further away from the site of OHCA. CONCLUSION: Survival after OHCA, where an AED was used, did not seem to differ in thinly, moderately and densely populated areas. The length of the AED retrieval distance, however, was correlated with reduced survival after adjusting for other potentially explanatory variables.

[Thrombolysis prior to thrombectomy in the treatment of patients with ischaemic stroke].

Patients with ischaemic stroke due to large vessel occlusion (LVO) are treated with thrombolysis before thrombectomy, if eligible, as recommended in current guidelines. However, new randomised controlled trials (RCTs) suggest, that pretreatment with thrombolysis may not be necessary in patients with LVO presenting directly at a thrombectomy-capable centre. In this review, we both gather the current knowledge on the treatment of ischaemic stroke due to LVO and evaluate on, whether this should be revised in the view of new RCTs.

Human skeletal muscle CD90+ fibro-adipogenic progenitors are associated with muscle degeneration in type 2 diabetic patients.

Type 2 diabetes mellitus (T2DM) is associated with impaired skeletal muscle function and degeneration of the skeletal muscles. However, the mechanisms underlying the degeneration are not well described in human skeletal muscle. Here we show that skeletal muscle of T2DM patients exhibit degenerative remodeling of the extracellular matrix that is associated with a selective increase of a subpopulation of fibro-adipogenic progenitors (FAPs) marked by expression of THY1 (CD90)-the FAPCD90+. We identify platelet-derived growth factor (PDGF) as a key FAP regulator, as it promotes proliferation and collagen production at the expense of adipogenesis. FAPsCD90+ display a PDGF-mimetic phenotype, with high proliferative activity, clonogenicity, and production of extracellular matrix. FAPCD90+ proliferation was reduced by in vitro treatment with metformin. Furthermore, metformin treatment reduced FAP content in T2DM patients. These data identify a PDGF-driven conversion of a subpopulation of FAPs as a key event in the fibrosis development in T2DM muscle.

Nampt controls skeletal muscle development by maintaining Ca2+ homeostasis and mitochondrial integrity.

OBJECTIVE: NAD+ is a co-factor and substrate for enzymes maintaining energy homeostasis. Nicotinamide phosphoribosyltransferase (NAMPT) controls NAD+ synthesis, and in skeletal muscle, NAD+ is essential for muscle integrity. However, the underlying molecular mechanisms by which NAD+ synthesis affects muscle health remain poorly understood. Thus, the objective of the current study was to delineate the role of NAMPT-mediated NAD+ biosynthesis in skeletal muscle development and function. METHODS: To determine the role of Nampt in muscle development and function, we generated skeletal muscle-specific Nampt KO (SMNKO) mice. We performed a comprehensive phenotypic characterization of the SMNKO mice, including metabolic measurements, histological examinations, and RNA sequencing analyses of skeletal muscle from SMNKO mice and WT littermates. RESULTS: SMNKO mice were smaller, with phenotypic changes in skeletal muscle, including reduced fiber area and increased number of centralized nuclei. The majority of SMNKO mice died prematurely. Transcriptomic analysis identified that the gene encoding the mitochondrial permeability transition pore (mPTP) regulator Cyclophilin D (Ppif) was upregulated in skeletal muscle of SMNKO mice from 2 weeks of age, with associated increased sensitivity of mitochondria to the Ca2+-stimulated mPTP opening. Treatment of SMNKO mice with the Cyclophilin D inhibitor, Cyclosporine A, increased membrane integrity, decreased the number of centralized nuclei, and increased survival. CONCLUSIONS: Our study demonstrates that NAMPT is crucial for maintaining cellular Ca2+ homeostasis and skeletal muscle development, which is vital for juvenile survival.

Isolation and characterization of muscle stem cells, fibro-adipogenic progenitors, and macrophages from human skeletal muscle biopsies.

Animal models clearly illustrate that the maintenance of skeletal muscle mass depends on the function and interaction of a heterogeneous population of resident and infiltrating mononuclear cells. Several lines of evidence suggest that mononuclear cells also play a role in muscle wasting in humans, and targeting these cells may open new treatment options for intervention or prevention in sarcopenia. Methodological and ethical constraints have perturbed exploration of the cellular characteristics and function of mononuclear cells in human skeletal muscle. Thus, investigations of cellular phenotypes often depend on immunohistochemical analysis of small tissue samples obtained by needle biopsies, which do not match the deep phenotyping of mononuclear cells obtained from animal models. Here, we have developed a protocol for fluorescence-activated cell sorting (FACS), based on single-cell RNA-sequencing data, for quantifying and characterizing mononuclear cell populations in human skeletal muscle. Muscle stem cells, fibro-adipogenic progenitors, and two subsets of macrophages (CD11c+/-) are present in needle biopsies in comparable quantities per milligram tissue to open surgical biopsies. We find that direct cell isolation is preferable due to a substantial shift in transcriptome when using preculture before the FACS procedure. Finally, in vitro validation of the cellular phenotype of muscle stem cells, fibro-adipogenic progenitors, and macrophages confirms population-specific traits. This study demonstrates that mononuclear cell populations can be quantified and subsequently analyzed from needle biopsy material and opens the perspective for future clinical studies of cellular mechanisms in muscle wasting.

Efficient correction of Duchenne muscular dystrophy mutations by SpCas9 and dual gRNAs.

CRISPR gene therapy is one promising approach for treatment of Duchenne muscular dystrophy (DMD), which is caused by a large spectrum of mutations in the dystrophin gene. To broaden CRISPR gene editing strategies for DMD treatment, we report the efficient restoration of dystrophin expression in induced myotubes by SpCas9 and dual guide RNAs (gRNAs). We first sequenced 32 deletion junctions generated by this editing method and revealed that non-homologous blunt-end joining represents the major indel type. Based on this predictive repair outcome, efficient in-frame deletion of a part of DMD exon 51 was achieved in HEK293T cells with plasmids expressing SpCas9 and dual gRNAs. More importantly, we further corrected a frameshift mutation in human DMD (exon45del) fibroblasts with SpCas9-dual gRNA ribonucleoproteins. The edited DMD fibroblasts were transdifferentiated into myotubes by lentiviral-mediated overexpression of a human MYOD transcription factor. Restoration of DMD expression at both the mRNA and protein levels was confirmed in the induced myotubes. With further development, the combination of SpCas9-dual gRNA-corrected DMD patient fibroblasts and transdifferentiation may provide a valuable therapeutic strategy for DMD.

Use and coverage of automated external defibrillators according to location in out-of-hospital cardiac arrest.

AIMS: To evaluate 1) the relative use of automated external defibrillators (AEDs) at different types of AED locations 2) the percentage of AEDs crossing location types during OHCA before use 3) the AED coverage distance at different types of AED locations, and 4) the 30-day-survival in different subgroups. METHODS: From 2014-2018, AEDs used by bystanders during out-of-hospital cardiac arrest (OHCA) in the Region of Southern Denmark were collected. Data regarding registered AEDs was retrieved from the national AED-network. The OHCA site and AED placement was categorized into; 1) Residential; 2) Public; 3) Nursing home, 4) Company/workplace; 5) Institution; 6) Health clinic and 7) Sports facility/recreational. To evaluate 30-day-survival, groups 4-7 were pooled into one Mixed group. RESULTS: In total 509 OHCAs were included. There was high relative usage of AEDs from public places, nursing homes, health clinics and sports facilities, and low relative usage from companies/workplaces, residential areas and institutions. Of AEDs used during residential OHCAs 39% were collected from public places. AEDs placed in residential areas and public places had a coverage of 575 m (IQR 130-1300) and 270 m (IQR5-550), respectively. Thirty-day- survival in public, residential and mixed groups were 49%, 14% and 67%, respectively. CONCLUSION: The relative use of AEDs from public places, nursing homes, sports facilities and health clinics was high, and AEDs used during OHCA in residential areas were most frequently collected from public places. AEDs placed in both residential areas and public places may have a wider coverage area than proposed in current literature.

A catalogue of PROMs in sports science: Quality assessment of PROM development and validation.

Choosing the most adequate PROM for a study is a non-trivial process. The aim of this study was to provide a catalogue with analyses of content and construct validity of PROMs relevant to research in sports science, including all published local translations. The most commonly used PROMs in sports research were selected from a PubMed search "patient reported outcome measures sports", identifying 439 articles and 194 different PROMs. Articles describing development of the 61 selected PROMs were assessed for content validity, and all articles regarding construct validity of each PROM and all published translations (in total 622 articles) were analyzed. A catalogue with assessments of the 61 PROMs was produced. The majority were of inferior validity, with few exceptions. The most common reason for this was that the PROM had not been developed by methods that ensure high content validity. Another major reason for inferior validity was that construct validity had not been secured by adequate statistical methods. In conclusion, this catalogue provides a tool for researchers to facilitate choosing the most valid PROM for studies in sports research. Furthermore, it shows for popular PROMs where further validation is needed, and for fields in musculoskeletal medicine where valid PROMs are lacking. It is suggested that a targeted effort is made to develop valid PROMs for major conditions in musculoskeletal research. The current method is easier to practice compared with assessment after COSMIN guidelines.

Combined Bone Marrow Aspirate and Platelet-Rich Plasma for Cartilage Repair: Two-Year Clinical Results.

PURPOSE: To evaluate the clinical and biological outcome of combined bone marrow aspirate concentrate (BMAC) and platelet-rich plasma (PRP) on a collagen scaffold for treating cartilage lesions in the knee. METHODS AND MATERIALS: Ten patients (mean age 29.4 years, range 18-36) suffering from large full-thickness cartilage in the knee were treated with BMAC and PRP from January 2015 to December 2016. In a 1-step procedure autologous BMAC and PRP was seeded onto a collagen scaffold and sutured into the debrided defect. Patients were evaluated by clinical outcome scores (IKDC [International Knee Documentation Committee Subjective Knee Form], KOOS [Knee Injury and Osteoarthritis Outcome Score], and pain score using the Numeric Rating Scale [NRS]) preoperatively, after 3 months, and after 1 and 2 years. Second-look arthroscopies were performed (n = 7) with biopsies of the repair tissue for histology. All patients had magnetic resonance imaging (MRI) preoperatively, after 1 year, and after 2 to 3.5 years with MOCART (magnetic resonance observation of cartilage repair tissue) scores evaluating cartilage repair. RESULTS: After 1 year significant improvements were found in IKDC, KOOS symptoms, KOOS ADL (Activities of Daily Living), KOOS QOL (Quality of Life), and pain at activity. At the latest follow-up significant improvements were seen in IKDC, KOOS symptoms, KOOS QOL, pain at rest, and pain at activity. MRI MOCART score for cartilage repair improved significantly from baseline to 1-year follow-up. Histomorphometry of repair tissue demonstrated a mixture of fibrous tissue (58%) and fibrocartilage (40%). CONCLUSION: Treatment of cartilage injuries using combined BMAC and PRP improved subjective clinical outcome scores and pain scores at 1 and 2 years postoperatively. MRI and histology indicated repair tissue inferior to the native hyaline cartilage.

How to translate and locally adapt a PROM. Assessment of cross-cultural differential item functioning.

Translating patient-reported outcome measures (PROMs) can alter the meaning of items and undermine the PROM's psychometric properties (quantified as cross-cultural differential item functioning [DIF]). The aim of this paper was to present the theoretical background for PROM translation, adaptation, and cross-cultural validation, and assess how PROMs used in sports medicine research have been translated and adapted. We also assessed DIF for the Knee Injury and Osteoarthritis Outcome Score (KOOS) across Danish, Norwegian, and Swedish versions. We conducted a search in PubMed and Scopus to identify the method of translation, adaptation, and validation of PROMs relevant to musculoskeletal research. Additionally, 150 preoperative KOOS questionnaires were obtained from the Scandinavian knee ligament reconstruction registries, and cross-cultural DIF was evaluated using confirmatory factor analysis and Rasch analysis. There were 392 studies identified, describing the translation of 61 PROMs. Ninety-four percent were performed with forward-backward technique. Forty-nine percent used cognitive interviews to ensure appropriate wording, understandability, and adaptation to the target culture. Only two percent were validated according to modern test theory. No study assessed cross-cultural DIF. One KOOS subscale showed no cross-cultural DIF, two had DIF with respect to some (but not all) items, and thus conversion tables could be constructed, and two KOOS subscales could not be pooled. Most PROM translations are of undocumented quality, despite the common conclusion that they are valid and reliable. Scores from three of five KOOS subscales can be pooled across the Danish, Norwegian, and Swedish versions, but two of these must be adjusted for DIF.

Responsiveness, minimal important difference, minimal relevant difference, and optimal number of patients for a study.

Several terms are used to describe changes in PROM scores in relation to treatments. Whether the change is small, large, or relevant is defined in different ways, yet these change scores are used to recommend or oppose treatments. They are also used to calculate the necessary number of patients for a study. This article offers a theoretical explanation behind the terms responsiveness, minimal important difference (MID), minimal important change (MIC), minimal relevant difference (MIREDIF), and threshold of clinical importance. It also gives instructions on how these and the optimal number of patients for a study are calculated. Responses to two domains of the Knee Injury and Osteoarthritis Outcome Score (KOOS), before and 1 year after reconstruction of the anterior cruciate ligament of 164 patients, are used to illustrate the calculations. This paper presents the most common methods used to calculate and interpret MID. Results vary substantially across domains, patient location on the scale, and health conditions. The optimal number of patients depends on the minimal relevant difference (MIREDIF), the standard error of the measure (SEM), the desired statistical power for the measurement, and the responsiveness of the measurement instrument (the PROM). There is often uncertainty surrounding the calculation and interpretation of responsiveness, MID, and MIREDIF, as these concepts are complex. When MID is used to evaluate research results, authors should specify how the MID was calculated, and its relevance for the study population. These measures should only be used after thorough consideration to justify healthcare decisions.

What is a PROM and why do we need it?

The purpose of this article was to introduce the reader to the nature of patient-reported outcome measures (PROMs) and pitfalls in their use. PROMs collect subjective information directly from the patient regarding specific or general conditions and add to clinical and functional outcomes, and turn unmeasurable subjective qualities into quantitative measures. PROMs are questionnaires consisting of items: questions or statements with predefined response options. The items in an adequate PROM have been developed by involvement of patients with the condition in focus, and the PROM has been validated for these patients using suitable statistical methods. An adequate well-targeted PROM is more responsive than an inadequate PROM. Unfortunately, many studies use inadequate PROMs as outcomes. The methods used to generate PROMs should be described as thoroughly as those used to develop any other types of measurement instruments, and the choice of PROM should always be explained and thereby justified. If the PROM used is not adequate, the consequences for the interpretation of the results should be discussed. In many cases, an adequate PROM does not exist. If the best available PROM is chosen, there are methods to validate the adequacy of the chosen PROM, which make an interpretation of the study results possible.

Psychometric validation of PROM instruments.

The aim was to provide an overview of the different statistical methods for validation of patient-reported outcome measures, ranging from simple statistical methods available in all software packages to advanced statistical models that require specialized software. A non-technical summary of classical test theory (CTT) and modern test theory (MTT) is provided. Specifically, confirmatory factor analysis, item response theory, and Rasch analysis is outlined. One CTT and three MTT methods were used to validate the two subscales (Symptoms and Quality of Life) from the Knee Injury and Osteoarthritis Outcome Score (KOOS). For each methodology, two analyses were considered: (i) a unidimensional analysis ignoring the pre-specified dimensionality, and (ii) a two-dimensional analysis using the pre-specified dimensionality. While CTT did not adequately address central issues regarding the validity of the KOOS subscales, the three MTT methods yielded very similar results. In conclusion, MTT methods offer analysis of all relevant properties related to the validity of patient-reported outcome measures, while this is not the case for CTT. Claims about sufficient validity based on CTT methods are inadequate and should not be trusted.

Choosing the most appropriate PROM for clinical studies in sports medicine.

Choosing the most appropriate patient-reported outcome measure (PROM) for a clinical study is essential in order to achieve trustworthy results. This choice will depend on (a) the objective of the study and hence the research question; (b) the choice of a theoretical framework, such as the World Health Organization's International Classification of Functioning, Disability, and Health (ICF); (c) whether there currently is a PROM that possesses high content validity and high construct validity for the specific patient group and objective, and if not; (d) the decision on whether to use a suboptimal PROM or develop and validate a new PROM. This paper presents the steps that should be followed in order to assess the relevance of PROMs and suggests ways to enhance the choice depending on the goal of the study.