Development of a Machine Learning Algorithm for Drug Screening Analysis on High-Resolution UPLC-MSE/QTOF Mass Spectrometry

BACKGROUND

Ultra-performance liquid chromatography (UPLC)-MSE/quadrupole time-of-flight (QTOF) high-resolution mass spectrometry employs untargeted, data-independent acquisition in a dual mode that simultaneously collects precursor ions and product ions at low and ramped collision energies, respectively. However, algorithmic analysis of large-scale multivariate data of comprehensive drug screening as well as the positivity criteria of drug identification have not been systematically investigated. It is also unclear whether ion ratio (IR), the intensity ratio of a defined product ion divided by the precursor ion, is a stable parameter that can be incorporated into the MSE/QTOF data analysis algorithm.

METHODS

IR of 91 drugs were experimentally determined and variation of IR was investigated across 5 concentrations measured on 3 different days. A data-driven machine learning approach was employed to develop multivariate linear regression (MLR) models incorporating mass error, retention time, number of detected fragment ions and IR, accuracy of isotope abundance, and peak response using drug-supplemented urine samples. Performance of the models was evaluated in an independent data set of unknown clinical urine samples in comparison with the results of manual analysis.

RESULTS

IR of most compounds acquired by MSE/QTOF were low and concentration-dependent (i.e., IR increased at higher concentrations). We developed an MLR model with composite score outputs incorporating 7 parameters to predict positive drug identification. The model achieved a mean accuracy of 89.38% in the validation set and 87.92% agreement in the test set.

CONCLUSIONS

The MLR model incorporating all contributing parameters can serve as a decision-support tool to facilitate objective drug identification using UPLC-MSE/QTOF.

MO241: Nets and Terminal Complement Pathway as Potential Biomarkers for Complement Overactivation Assessment in Anca-Associated Vasculitis

BACKGROUND AND AIMS

Clinical, in vitro, and animal model-derived evidence has demonstrated a critical involvement of the alternative complement pathway (aCP) in the pathogenesis of ANCA-associated vasculitis (AAV). In this regard, neutrophil extracellular traps (NETs) have been suggested to be a key element between ANCA-induced neutrophil activation and aCP [1]. However, the role of the terminal complement pathway (tCP) is less well studied [2].

METHOD

A prospective, observational, multicenter study analyzing first episodes and relapses of patients with AAV, with a minimum follow-up of 6 months, was performed. Blood samples were collected at diagnosis (AAV-t1) and at remission (AAV-t2). Control population consisted of age and sex-matched individuals. Complement activation was assessed by analyzing the complement membrane attack complex (C5b-9) deposition on cultured endothelial cells (HMEC-1), by immunofluorescence, after exposing them to activated plasma (a-plasma: obtained by mixing patient's citrated plasma with healthy subjects’ sera pool, 1:1). C5b-9 deposits induced by patients’ a-plasma were calculated as percentage of labeled area with respect to the total area analyzed. Results from patient and control samples were expressed as fold increase (mean ± SEM) versus those obtained with the pool of a-plasma from healthy subjects. Plasma levels of tCP and aCP soluble factors, such as sC5b-9 and sFBb (respectively), were also measured (mean ± SEM). Circulating NETs were indirectly measured by quantifying circulant dsDNA plasmatic concentration (mean ± SEM) as a NET surrogate.

RESULTS

The present results were obtained with samples from 13 AAV-MPO patients who achieved complete remission (38% men, age 63 ± 14 years) and 10 controls (45% men, age 66 ± 6 years). At AAV-t1, there was a statistically significant increase (P < .05) of C5b-9 deposition on HMEC-1 in response to patients’ a-plasma (fold increase of 5.3 ± 1.3) compared with control samples (fold increase of 1.2 ± 0.2). Samples obtained at AAV-t2 induced less C5b-9 deposition than at AAV-t1 (fold increase of 0.9 ± 0.2; P < .05), with values similar to controls. Regarding soluble factors, levels of both sC5b-9 and sFBb were significantly increased in AAV-t1 (1882 ± 418 ng/mL and 3.2 ± 0.4 µg/mL, respectively; P < .05) versus AAV-t2 (852 ± 104 ng/mL and 1.9 ± 0.2 µg/mL, respectively; P < .05). At AAV-t2, levels were similar to controls (708 ± 42 ng/mL for sC5b-9 and 2.4 ± 0.2 µg/mL for sFBb). Circulating NETs were also increased in AAV-t1 (22.2 ± 3.5 µg/mL) compared with both AAV-t2 and controls (13.6 ± 1.1 µg/mL and 13.7 ± 0.3 µg/mL, respectively; P < .05). Moreover, NETs in AAV-t1 presented a significant correlation with sFBb levels, both in AAV-t1 (r = 0.709; P < .05) and in AAV-t2 (r = 0.585; P < .05).

CONCLUSION

There is a relationship between NETs, AAV activity and sFBb, which supports the role of NETs and cAP in AAV pathogenesis. Moreover, differences in C5b-9 deposition between the two stages of the disease suggest that tCP may be dysregulated in AAV. Further characterization of this dysregulation may lead to new diagnostic or disease activity biomarkers, as well as new therapeutic options for the management of patients with AAV.

Critically ill COVID-19 patients attended by anesthesiologists in northwestern Spain: a multicenter prospective observational study

BACKGROUND AND OBJECTIVES

There are limited information on outcome, complications and treatments of critically ill COVID-19 patients requiring admission to an intensive care unit (ICU). The aim of this study is to describe the clinical ICU course, treatments used, complications and outcomes, of critically ill COVID-19 patients admitted in seven ICU in Galicia region during the 2020 March-April pandemic peak.

METHODS

Between March 21 and April 19, 2020, we evaluated critically ill COVID-19 patients admitted to the ICU of Anesthesia of seven hospitals in Galicia, northwestern Spain. Outcome, complications, and treatments were monitored until May 6, 2020, the final date of follow-up.

RESULTS

A total of 97 critically ill COVID-19 patients were included. During ICU stay, mechanical ventilation became necessary in 80 (82.5%) patients, and tracheostomy in 22 (22.7%) patients. Prone position was used frequently in both intubated (67.5%) and awake (27.8%) patients. Medications consisted of antivirals agents (92.7%), corticosteroids (93.8%), tocilizumab (57.7%), and intermediate or high doses of anticoagulants (83.5%). The most frequent complications were ICU-acquired infection (52.6%), thrombosis events (16.5%), and reintubation (9.3%). After a median follow-up of 42 (34-45) days, 15 patients (15.5%) deceased, 73 patients (75.2%) had been discharged from ICU, and nine patients (9.3%) were still in the ICU.

CONCLUSIONS

A high proportion of our critically ill COVID-19 patients required mechanical ventilation, prone positioning, antiviral medication, corticosteroids, and anticoagulants. ICU complications were frequent, mainly infections and thrombotic events. We had a relatively low mortality of 15,5%.

Vertebral fracture risk in glucocorticoid-induced osteoporosis: the role of hypogonadism and corticosteroid boluses

OBJECTIVE

The aim of this study was to identify the risk factors associated with fragility fracture (FF) development in glucocorticoid (GC)-treated patients.

METHODS

127 patients (aged 62±18 years, 63% women) on GC-treatment (mean dose 14.5±14.1 mg/day and duration 47.7±69 months) were included. The clinical data collected included bone metabolism study (including gonadal axis), GC-treatment, disease activity, dual-energy X-ray absorptiometry analysis (evaluating densitometric osteoporosis (OP) and trabecular bone score (TBS) degraded microarchitecture values (DMA)), X-ray (assessing vertebral fractures (VF)), FRAX risk (GC-adjusted) and previous FF.

RESULTS

17% of the patients had VF, 28% FF (VF and/or non-VF), 29% OP and 52% DMA. Patients with VF received more GC boluses (57.1% vs 29.5%, p=0.03), were older (68±13 vs 60±19 years, p=0.02), postmenopausal (100% vs 67%, p=0.02), had low testosterone levels (57% vs 11%, p=0.02), lower TBS values (1.119±0.03 vs 1.237±0.013, p<0.001) and higher FRAX risk (17.2±16 vs 9.3±7.6, p=0.003). Patients with FF showed higher accumulated GC doses (16.6±18.4 vs 11.1±12.9 g, p=0.046). On multivariate analysis, hypogonadism (OR 12.38; 95% CI 1.85 to >100, p=0.01) and having received GC boluses (OR 3.45; 95% CI 1.04 to 12.15, p=0.01) were the main factors related to VF. Hypogonadism (OR 7.03; 95% CI 1.47 to 38.37, p=0.01) and FRAX >20 (OR 7.08; 95% CI 1.28 to 53.71, p=0.02) were factors related to FF.

CONCLUSION

Hypogonadism is the principal risk factor for developing fractures in GC-treated men and women, whereas receiving GC boluses is a major factor for VF. These results indicate the importance of evaluating the gonadal axis in these patients.

Association between vitamin D deficiency and common variants of Vitamin D binding protein gene among Mexican Mestizo and indigenous postmenopausal women

PURPOSE

Vitamin D deficiency (VDD) and polymorphisms in the group-specific component (GC) gene are known to be associated in different populations. However, the effects of such genetic variants may vary across different populations. Thus, the objective of this study was to estimate the association between Vitamin D-Binding Protein (VDBP) haplotypes and VDD in mestizo postmenopausal women and Mexican Amerindian ethnic groups.

METHODS

This was a cross-sectional study of 726 postmenopausal Mexican women from the Health Workers Cohort Study (HWCS) and 166 postmenopausal women from the Metabolic Analysis in an Indigenous Sample (MAIS) cohort in Mexico. GC polymorphisms (rs7045 and rs4588) were analyzed by TaqMan probes. Serum 25-hydroxyvitamin D [25(OH)D] levels were measured by Chemiluminescent Microparticle Immuno Assay.

RESULTS

The prevalence of VDD serum 25(OH)D < 20 ng/mL was 43.7% in mestizo women and 44.6% in indigenous women. In HWCS, the single nucleotide polymorphisms (SNPs) rs7041 and rs4588 were associated with VDD. In addition, women from the HWCS, carrying the haplotypes GC2/2 and GC1f/2 had higher odds of VDD (OR = 2.83, 95% CI 1.14, 7.02; and OR = 2.30, 95% CI 1.40, 3.78, respectively) compared to women with haplotype 1f/1 s. These associations were not statistically significant in the MAIS cohort.

CONCLUSIONS

Our results show genetic association of the analyzed SNPs and related haplotypes, on the GC gene, with VDD in mestizo Mexican postmenopausal women. Moreover, a high prevalence of VDD with high genetic variability within the country was observed. Our results support the need for national policies for preventing VDD.

Automatic speech analysis to early detect functional cognitive decline in elderly population

This study aimed at evaluating whether people with a normal cognitive function can be discriminated from subjects with a mild impairment of cognitive function based on a set of acoustic features derived from spontaneous speech. Voice recordings from 90 Italian subjects (age >65 years; group 1: 47 subjects with MMSE>26; group 2: 43 subjects with 20≤ MMSE ≤26) were collected. Voice samples were processed using a MATLAB-based custom software to derive a broad set of known acoustic features. Linear mixed model analyses were performed to select the features able to significantly distinguish between groups. The selected features (% of unvoiced segments, duration of unvoiced segments, % of voice breaks, speech rate, and duration of syllables), alone or in addition to age and years of education, were used to build a learning-based classifier. The leave-one-out cross validation was used for testing and the classifier accuracy was computed. When the voice features were used alone, an overall classification accuracy of 0.73 was achieved. When age and years of education were additionally used, the overall accuracy increased up to 0.80. These performances were lower than the accuracy of 0.86 found in a recent study. However, in that study the classification was based on several tasks, including more cognitive demanding tasks. Our results are encouraging because acoustic features, derived for the first time only from an ecologic continuous speech task, were able to discriminate people with a normal cognitive function from people with a mild cognitive decline. This study poses the basis for the development of a mobile application performing automatic voice analysis on-the-fly during phone calls, which might potentially support the detection of early signs of functional cognitive decline.

Management of Takayasu arteritis: a systematic literature review informing the 2018 update of the EULAR recommendation for the management of large vessel vasculitis

Objective

To collect available evidence on management of large vessel vasculitis to inform the 2018 update of the EULAR management recommendations.

Methods

Two independent systematic literature reviews were performed, one on diagnosis and monitoring and the other on drugs and surgical treatments. Using a predefined PICO (population, intervention, comparator and outcome) strategy, Medline, Embase and Cochrane databases were accessed. Eligible papers were reviewed and results condensed into a summary of findings table. This paper reports the main results for Takayasu arteritis (TAK).

Results

A total of 287 articles were selected. Relevant heterogeneity precluded meta-analysis. Males appear to have more complications than females. The presence of major complications, older age, a progressive disease course and a weaker inflammatory response are associated with a more unfavourable prognosis. Evidence for details on the best disease monitoring scheme was not found. High-quality evidence to guide the treatment of TAK was not found. Glucocorticoids are widely accepted as first-line treatment. Conventional immunosuppressive drugs and tumour necrosis factor inhibitors were beneficial in case series and uncontrolled studies. Tocilizumab failed the primary endpoint (time to relapse) in a randomised controlled clinical trial; however, results still favoured tocilizumab over placebo. Vascular procedures may be required, and outcome is better when performed during inactive disease.

Conclusions

Evidence to guide monitoring and treatment of patients with TAK is predominantly derived from observational studies with low level of evidence. Therefore, higher-quality studies are needed in the future.

Systematic literature review informing the 2018 update of the EULAR recommendation for the management of large vessel vasculitis: focus on giant cell arteritis

Objectives

To analyse the current evidence for the management of large vessel vasculitis (LVV) to inform the 2018 update of the EULAR recommendations.

Methods

Two systematic literature reviews (SLRs) dealing with diagnosis/monitoring and treatment strategies for LVV, respectively, were performed. Medline, Embase and Cochrane databases were searched from inception to 31 December 2017. Evidence on imaging was excluded as recently published in dedicated EULAR recommendations. This paper focuses on the data relevant to giant cell arteritis (GCA).

Results

We identified 287 eligible articles (122 studies focused on diagnosis/monitoring, 165 on treatment). The implementation of a fast-track approach to diagnosis significantly lowers the risk of permanent visual loss compared with historical cohorts (level of evidence, LoE 2b). Reliable diagnostic or prognostic biomarkers for GCA are still not available (LoE 3b).The SLR confirms the efficacy of prompt initiation of glucocorticoids (GC). There is no high-quality evidence on the most appropriate starting dose, route of administration, tapering and duration of GC (LoE 4). Patients with GCA are at increased risk of dose-dependent GC-related adverse events (LoE 3b). The addition of methotrexate or tocilizumab reduces relapse rates and GC requirements (LoE 1b). There is no consistent evidence that initiating antiplatelet agents at diagnosis would prevent future ischaemic events (LoE 2a). There is little evidence to guide monitoring of patients with GCA.

Conclusions

Results from two SLRs identified novel evidence on the management of GCA to guide the 2018 update of the EULAR recommendations on the management of LVV.

Validation of the EULAR/ERA-EDTA recommendations for the management of ANCA-associated vasculitis by disease content experts

The European League Against Rheumatism recommendations for the management of antineutrophil cytoplasmic antibody-associated vasculitis have been recently published. Unique to recommendation development, they were also voted on by members of a learned society. This paper explores the wider validity of the recommendations among people who self-identify as clinicians caring for patients with vasculitis. In addition to the task force, a learned society (European Vasculitis Society—EUVAS) was invited, through online survey, to rate independently the strength of evidence of each recommendation to obtain an indication of the agreement among the final target audience and ultimate end-users of the recommendations. The survey took place in June 2015. Of the 158 EUVAS members surveyed, there were 88 responses (55.7%). There was a large degree of agreement in the voting patterns between EUVAS survey participants and task force members. Notable exceptions were lower grades for the recommendation of the use of rituximab for remission induction in patients with eosinophilic granulomatosis with polyangiitis and for methotrexate and mycophenolate mofetil as remission maintenance agents in patients with granulomatosis with polyangiitis/microscopic polyangiitis by EUVAS members. These results are encouraging and suggest that the voting patterns of the task force are representative of the wider vasculitis community. We recommend future recommendations adopt this approach for data/expert-based treatment guidelines, especially for multisystem diseases.

2015 recommendations for the management of polymyalgia rheumatica: a European League Against Rheumatism/American College of Rheumatology collaborative initiative

Therapy for polymyalgia rheumatica (PMR) varies widely in clinical practice as international recommendations for PMR treatment are not currently available. In this paper, we report the 2015 European League Against Rheumatism (EULAR)/American College of Rheumatology (ACR) recommendations for the management of PMR. We used the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology as a framework for the project. Accordingly, the direction and strength of the recommendations are based on the quality of evidence, the balance between desirable and undesirable effects, patients' and clinicians' values and preferences, and resource use. Eight overarching principles and nine specific recommendations were developed covering several aspects of PMR, including basic and follow-up investigations of patients under treatment, risk factor assessment, medical access for patients and specialist referral, treatment strategies such as initial glucocorticoid (GC) doses and subsequent tapering regimens, use of intramuscular GCs and disease modifying anti-rheumatic drugs (DMARDs), as well as the roles of non-steroidal anti-rheumatic drugs and non-pharmacological interventions. These recommendations will inform primary, secondary and tertiary care physicians about an international consensus on the management of PMR. These recommendations should serve to inform clinicians about best practices in the care of patients with PMR.

Estimated glomerular filtration rate (eGFR), 25(OH) D3, chronic kidney disease (CKD), the MYH9 (myosin heavy chain 9) gene in old and very elderly people

It is known that the common physiological denominator of the ageing process is an attenuation of functional performance with respect to the situation of young people and adults. However, since the first cohort-based longitudinal studies, it has not been possible to establish a "linear" relationship between age and glomerular filtration in all cases. This does not mean that there is no physiological ageing process at all; in addition to those already elucidated, its mechanisms include cell senescence, podocyte dysfunction, a vitamin D deficiency, and homozygotic forms of the MYH9 gene. The aim of the present work was to analyse the prevalence of chronic kidney disease (CKD) and, where possible, the correlation between CKD, defined by an eGFR < 60 ml/min/1.73 m(2), plasma 25(OH)D3 levels and the MYH9 gene in a population of elderly and very elderly persons. These parameters have not been evaluated previously in populations of elderly and very elderly patients. It is concluded that a moderate decrease in the eGFR occurs with age. This does not imply the presence of CKD in elderly people, since in most individuals the reduced eGFR is not accompanied by anaemia, and no individuals show hypocalcaemia, hyperphosphataemia or a high Alb/Cr ratio. Here we observed a lower Hb level and an elevated Alb/Cr ratio in subjects heterozygotic for the MYH9 gene. This could be interpreted in the sense that the gene could exert some protective effect on renal function, whereas the heterozygotic form (allele A) of the MYH9 gene could be considered a very early marker, a new risk factor for the appearance of CKD, or a sign of renal frailty in elderly people.

Gait analysis of myopathic children in relation to impairment level and energy cost

The electromyographic and kinematic patterns of gait and its energy cost were studied in 12 myopathic patients who were still walking and 12 normal subjects. On the basis of significant gait variables, three distinct levels of impairment were defined in the group of myopathic subjects: early, intermediate and final. These clusterings were predicted with 95.7% accuracy by two gait variables: the stance phase duration and the heel vertical excursion. The gait patterns of each group were compared to the control group. Reduced speed and range of motion, short stride length, small foot-floor clearance, increased energy cost and lateral displacements of centre of gravity were typical and increased with the muscular weakness. The activation of soleus muscle occurred progressively earlier as did the cessation of tibialis anterior activity. In severe disorders, there was increased activity in the muscles acting on the hip and knee. When muscular dystrophy leads to more disability the myopathic patients tended to change from the normal plantigrade gait pattern to an infantile digitigrade-like pattern with a decrease of the tibialis anterior muscle work.

Citrus mealybug (Hemiptera: Pseudococcidae) movement and population dynamics in an arbor-trained vineyard

The citrus mealybug, Planococcus citri (Risso) (Hemiptera: Pseudococcidae), is the main grapevine pest in vineyards in some countries, such as Spain and Brazil. In Galician vineyards (northwestern Spain), mealybug population levels are low because the accumulated degree-days are lower than in other grapevine-growing areas. The main problem caused by mealybugs is the transmission of viruses, even at low infestation levels. The active period of citrus mealybug in the study vineyard lasted from July until December, with an important movement peak at the end of July and August and a lower peak in November. The mealybug mainly moved upward along arbor-trained plants, and there were no important downward movements at the end of the season as has been described for other grapevine mealybugs. The mealybugs were normally restricted to the woody organs and were only present on leaves, branches, and green canes (always close to woody parts) in plants with high infestations. The movement of mealybugs between plants does not seem to take place by contact between green organs. Passive aerial transport and movement of pruning remains may play an important role in mealybug movement and thus in spread of the virus. The number of mealybugs carrying Grapevine leafroll-associated virus 3 (GLRaV-3) was found to represent approximately 75% of mealybugs caught in a GLRaV-3 infected vineyard.

Outcomes from studies of antineutrophil cytoplasm antibody associated vasculitis: a systematic review by the European League Against Rheumatism systemic vasculitis task force

OBJECTIVES

We undertook a systematic literature review as a background to the European League Against Rheumatism (EULAR) recommendations for conducting clinical trials in anti-neutrophil cytoplasm antibody associated vasculitis (AAV), and to assess the quality of evidence for outcome measures in AAV.

METHODS

Using a systematic Medline search, we categorised the identified studies according to diagnoses. Factors affecting remission, relapse, renal function and overall survival were identified.

RESULTS

A total of 44 papers were reviewed from 502 identified by our search criteria. There was considerable inconsistency in definitions of end points. Remission rates varied from 30% to 93% in Wegener granulomatosis (WG), 75% to 89% in microscopic polyangiitis (MPA) and 81% to 91% in Churg-Strauss syndrome (CSS). The 5-year survival for WG, MPA and CSS was 74-91%, 45-76% and 60-97%. Relapse (variably defined) was common in the first 2 years but the frequency varied: 18% to 60% in WG, 8% in MPA, and 35% in CSS. The rate of renal survival in WG varied from 23% at 15 months to 23% at 120 months.

METHOD

used to assess morbidity varied between studies. Ignoring the variations in definitions of the stage of disease, factors influencing remission, relapse, renal and overall survival included immunosuppressive therapy used, type of organ involvement, presence of ANCA, older age and male gender.

CONCLUSIONS

Factors influencing remission, relapse, renal and overall survival include the type of immunosuppressive therapy used, pattern of organ involvement, presence of ANCA, older age and male gender. Methodological variations between studies highlight the need for a consensus on terminology and definitions for future conduct of clinical studies in AAV.