PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks.

MOTIVATION: Accurate quantitative information about protein abundance is crucial for understanding a biological system and its dynamics. Protein abundance is commonly estimated using label-free, bottom-up mass spectrometry (MS) protocols. Here, proteins are digested into peptides before quantification via MS. However, missing peptide abundance values, which can make up more than 50% of all abundance values, are a common issue. They result in missing protein abundance values, which then hinder accurate and reliable downstream analyses. RESULTS: To impute missing abundance values, we propose PEPerMINT, a graph neural network model working directly on the peptide level that flexibly takes both peptide-to-protein relationships in a graph format as well as amino acid sequence information into account. We benchmark our method against 11 common imputation methods on 6 diverse datasets, including cell lines, tissue, and plasma samples. We observe that PEPerMINT consistently outperforms other imputation methods. Its prediction performance remains high for varying degrees of missingness, different evaluation approaches, and differential expression prediction. As an additional novel feature, PEPerMINT provides meaningful uncertainty estimates and allows for tailoring imputation to the user's needs based on the reliability of imputed values. AVAILABILITY AND IMPLEMENTATION: The code is available at https://github.com/DILiS-lab/pepermint.

Maternal and fetal outcomes in pregnancy complicated by pre-existing lupus nephritis: Insights from a developing country Pakistan.

BACKGROUND: Pregnancy in women with systemic lupus erythematosus (SLE) has remained a great challenge for clinicians in terms of maternal and fetal outcomes. The outcomes in women with pre-existing lupus nephritis (LN) are variable. The impact of different classes of LN on maternal and fetal outcomes during pregnancy is not well defined, as data is very scarce, especially from the developing countries. METHODS: A retrospective analysis was conducted on 52 women with 89 pregnancies. All had biopsy-proven LN. Those women who conceived at least 6 months after the diagnosis were included. The analysis was conducted between July 1998 and June 2018 at Sindh Institute of Urology and Transplantation (SIUT), evaluating the outcomes for both the mother and the fetus with a minimum follow-up of 12 months after child birth. RESULTS: The mean maternal age at SLE diagnosis was 21.45 ± 6 years and at first pregnancy was 26.49 ± 5.63 years. The mean disease duration was 14.02 ± 19.8 months. At conception, 47 (52.8%) women were hypertensive, 9 (10%) had active disease while 38 (42.7%) and 42 (47.2%) were in complete and partial remission, respectively. A total of 17 (19.1%) were on mycophenolate mofetil (MMF), which was switched to azathioprine (AZA). Out of 89 pregnancies, 56 (62.9%) were successful, while 33 (37.07%) had fetal complications like spontaneous abortion, stillbirth, perinatal death, and intrauterine growth retardation (IUGR). There were more vaginal deliveries (33 [58.92%]) than caesarean sections (23 [41.07%]). Renal flare was observed in 33 (37.1%) women while 15 (16.9%) developed pre-eclampsia. Proliferative LN was found in 56 (62.9%) cases, but no significant differences were found in maternal and fetal outcomes in relation to LN classes (p = .58). However, disease outcomes at 12 months were significantly poor in those with active disease at the time of conception (p < .05). There was only one maternal death. A total of 10 (11.2%) women showed deterioration in renal function and 5 (5.6%) were dialysis-dependent at 12 months. CONCLUSION: The maternal and fetal outcomes in pre-existing LN depend on the disease activity at the time of conception. No correlation was found between International Society of Nephrology/Renal Pathology Society (ISN/RPS) classes of LN and adverse disease and pregnancy outcomes.

Interventions Based on Behavior Change Techniques to Encourage Physical Activity or Decrease Sedentary Behavior in Community-Dwelling Adults Aged 50-70: Systematic Review With Intervention Component Analysis.

Increasing physical activity (PA) and/or decreasing sedentary behaviors is important in the delay and prevention of long-term conditions. PA can help maintain function and independence and decrease the need for hospitalization/institutionalization. Activity rates often decline in later life resulting in a need for interventions that encourage uptake and adherence through the use of Behavior Change Techniques (BCTs). We conducted a systematic review of the evidence for interventions that included BCTs in community-dwelling adults with a mean age of 50-70. The review followed PRISMA guidelines. The interventions were psychosocial, nonpharmacological, and noninvasive interventions utilizing components based on BCTs that evaluated change in PA and/or sedentary behavior. Intervention Component Analysis (ICA) was used to synthesize effectiveness of intervention components. Twelve randomized controlled trials were included in this review. The mean sample age was 50-64. Thirteen BCTs were used across all studies, and the most commonly used techniques were goals and planning, feedback and monitoring, and natural consequences. Seven intervention components linked with BCTs were found: personalized goal setting, tailored feedback from facilitators, on-site and postintervention support, education materials and resources, reinforcing change on behavior and attitudes, self-reported monitoring, and social connectedness. All components, except for social connectedness, were associated with improved health behavior and PA levels. The interventions that use BCTs have incorporated strategies that reinforce change in behavior and attitudes toward PA.

Proteomics-Based Mapping of Bronchopulmonary Dysplasia-Associated Changes in Noninvasively Accessible Oral Secretions.

OBJECTIVE: To determine if oral secretions (OS) can be used as a noninvasively collected body fluid, in lieu of tracheal aspirates (TA), to track respiratory status and predict bronchopulmonary dysplasia (BPD) development in infants born <32 weeks. STUDY DESIGN: This was a retrospective, single center cohort study that included data and convenience samples from week-of-life (WoL) 3 from 2 independent preterm infant cohorts. Using previously banked samples, we applied our sample-sparing, high-throughput proteomics technology to compare OS and TA proteomes in infants born <32 weeks admitted to the Neonatal Intensive Care Unit (NICU) (Cohort 1; n = 23 infants). In a separate similar cohort, we mapped the BPD-associated changes in the OS proteome (Cohort 2; n = 17 infants including 8 with BPD). RESULTS: In samples collected during the first month of life, we identified 607 proteins unique to OS, 327 proteins unique to TA, and 687 overlapping proteins belonging to pathways involved in immune effector processes, neutrophil degranulation, leukocyte mediated immunity, and metabolic processes. Furthermore, we identified 37 OS proteins that showed significantly differential abundance between BPD cases and controls: 13 were associated with metabolic and immune dysregulation, 10 of which (eg, SERPINC1, CSTA, BPI) have been linked to BPD or other prematurity-related lung disease based on blood or TA investigations, but not OS. CONCLUSIONS: OS are a noninvasive, easily accessible alternative to TA and amenable to high-throughput proteomic analysis in preterm newborns. OS samples hold promise to yield actionable biomarkers of BPD development, particularly for prospective categorization and timely tailored treatment of at-risk infants with novel therapies.

The Use of Digital Health by South Asian Communities: Scoping Review.

BACKGROUND: South Asian individuals experience a higher burden of chronic diseases and limited access to health care services compared with their Caucasian peers. Digital health interventions can enhance the delivery of health care, minimize health inequities, and consequently improve health status among minority ethnic groups. However, it is unclear how South Asian people view and perceive the use of digital health technologies to support their health needs. OBJECTIVE: The aim of the review is to identify South Asian individuals' experiences and attitudes of digital health and explore the barriers and facilitators affecting their use of digital health services. METHODS: The Arksey and O'Malley methodological framework was used to guide this scoping review. Five electronic databases were examined for pertinent papers, which were augmented by searching bibliographies of the retrieved papers and gray literature. A total of 1328 potentially relevant papers were retrieved from the initial search, and the supplemental search added 7 papers to the final list of potentially included papers. Each paper on the initial inclusion list was independently reviewed, leaving 15 papers to be included in the review. RESULTS: Data were analyzed thematically leading to the development of two overarching themes: (1) barriers to uptake of digital health and (2) facilitators of use of digital health services. There was a general consensus that South Asian communities still struggle with inadequate access to digital health technologies. Some studies suggest multiple initiatives to improve accessibility and acceptability of digital health services within South Asian communities in order to mitigate health disparities and develop a more inclusive health care system. These include the development of multiple-language and culturally sensitive interventions and digital skill development sessions. Most studies were conducted in South Asian countries, focusing on measurable outcomes of digital health interventions. Few explored the experiences and views of South Asian community members residing in the West as a minority ethnic group, for example, British South Asians. CONCLUSIONS: Literature mapping proposes that South Asian people frequently struggle with a health care system that may limit their access to digital health services, and sometimes fails to consider social and cultural needs. There is growing evidence that digital health interventions have the potential to facilitate supported self-management, which is part of the plans to adopt person-centered care. These interventions are particularly important for overcoming some of the challenges, for example, time constraints, safety, and gender sensitivity, associated with the delivery of health care interventions in minority ethnic groups such as South Asians in the United Kingdom, and thus to improve minority ethnic groups' access to health care services to support individual health needs, and consequently enhance health status.

Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility.

The Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB are essential for growth and have been proposed as possible drug targets. We used a titratable conditional depletion system to investigate the functions of these kinases. Depletion of PknA or PknB or both kinases resulted in growth arrest, shortening of cells, and time-dependent loss of acid-fast staining with a concomitant decrease in mycolate synthesis and accumulation of trehalose monomycolate. Depletion of PknA and/or PknB resulted in markedly increased susceptibility to ß-lactam antibiotics, and to the key tuberculosis drug rifampin. Phosphoproteomic analysis showed extensive changes in protein phosphorylation in response to PknA depletion and comparatively fewer changes with PknB depletion. These results identify candidate substrates of each kinase and suggest specific and coordinate roles for PknA and PknB in regulating multiple essential physiologies. These findings support these kinases as targets for new antituberculosis drugs and provide a valuable resource for targeted investigation of mechanisms by which protein phosphorylation regulates pathways required for growth and virulence in M. tuberculosis.

Using plasma proteomics to investigate viral infections of the central nervous system including patients with HIV-associated neurocognitive disorders.

State-of-the-art liquid chromatography/mass spectrometry (LC/MS)-based proteomic technologies, using microliter amounts of patient plasma, can detect and quantify several hundred plasma proteins in a high throughput fashion, allowing for the discovery of clinically relevant protein biomarkers and insights into the underlying pathobiological processes. Using such an in-house developed high throughput plasma proteomics allowed us to identify and quantify > 400 plasmas proteins in 15 min per sample, i.e., a throughput of 100 samples/day. We demonstrated the clinical applicability of our method in this pilot study by mapping the plasma proteomes from patients infected with human immunodeficiency virus (HIV) or herpes virus, both groups with involvement of the central nervous system (CNS). We found significant disease-specific differences in the plasma proteomes. The most notable difference was a decrease in the levels of several coagulation-associated proteins in HIV vs. herpes virus, among other dysregulated biological pathways providing insight into the differential pathophysiology of HIV compared to herpes virus infection. In a subsequent analysis, we found several plasma proteins associated with immunity and metabolism to differentiate patients with HIV-associated neurocognitive disorders (HAND) compared to cognitively normal people with HIV (PWH), suggesting the presence of plasma-based biomarkers to distinguishing HAND from cognitively normal PWH. Overall, our high-throughput plasma proteomics pipeline enables the identification of distinct proteomic signatures of HIV and herpes virus, which may help illuminate divergent pathophysiology behind virus-associated neurological disorders.

The impact of COVID-19 lockdowns on physical activity amongst older adults: evidence from longitudinal data in the UK.

BACKGROUND: A sedentary lifestyle increases the risk of adverse health outcomes and frailty,particularly for older adults. To reduce transmission during the COVID-19 pandemic, people were instructed to stay at home, group sports were suspended, and gyms were closed, thereby limiting opportunities for physical activity. Whilst evidence suggests that physical activity levels reduced during the pandemic, it is unclear whether the proportion of older adults realising the recommended minimum level of physical activity changed throughout the various stages of lockdown. METHODS: We used a large sample of 3,660 older adults (aged ≥ 65) who took part in the UK Household Longitudinal Study's annual and COVID-19 studies. We examined changes in the proportion of older adults who were realising the UK Chief Medical Officers' physical activity recommendations for health maintenance at several time points before and after COVID-19 lockdowns were imposed. We stratified these trends by the presence of health conditions, age, neighbourhood deprivation, and pre-pandemic activity levels. RESULTS: There was a marked decline in older adults' physical activity levels during the third national lockdown in January 2021. The proportion realising the Chief Medical Officers' physical activity recommendations decreased from 43% in September 2020 to 33% in January 2021. This decrease in physical activity occurred regardless of health condition, age, neighbourhood deprivation, or pre-pandemic activity levels. Those doing the least activity pre-lockdown increased their activity during lockdowns and those doing the most decreased their activity levels. CONCLUSIONS: Reductions in older adults' physical activity levels during COVID-19 lockdowns have put them at risk of becoming deconditioned and developing adverse health outcomes. Resources should be allocated to promote the uptake of physical activity in older adults to reverse the effects of deconditioning.

Women's perceptions of PERSPECTIVE: a breast cancer risk stratification e-platform.

BACKGROUND: Breast cancer risk stratification categorizes a woman's potential risk of developing the disease as near-population, intermediate, or high. In accordance, screening and follow up for breast cancer can readily be tailored following risk assessment. Recent efforts have focussed on developing more accessible means to convey this information to women. This study sought to document the relevance of an informational e-platform developed for these purposes. OBJECTIVE: To begin to assess a newly developed breast cancer risk stratification and decision support e-platform called PERSPECTIVE (PErsonalised Risk Stratification for Prevention and Early deteCTIon of breast cancer) among women who do not know their personal breast cancer risk (Phase 1). Changes (pre- and post- e-platform exposure) in knowledge of breast cancer risk and interest in undergoing genetic testing were assessed in addition to perceptions of platform usability and acceptability. METHODS: Using a pre-post design, women (N = 156) of differing literacy and education levels, aged 30 to 60, with no previous breast cancer diagnosis were recruited from the general population and completed self-report e-questionnaires. RESULTS: Mean e-platform viewing time was 18.67 min (SD 0.65) with the most frequently visited pages being breast cancer-related risk factors and risk assessment. Post-exposure, participants reported  significantly higher breast cancer-related knowledge (p < .001). Increases in knowledge relating to obesity, alcohol, breast density, menstruation, and the risk estimation process remained even when sociodemographic variables age and education were controlled. There were no significant changes in genetic testing interest post-exposure. Mean ratings for e-platform acceptability and usability were high: 26.19 out of 30 (SD 0.157) and 42.85 out of 50 (SD 0.267), respectively. CONCLUSIONS: An informative breast cancer risk stratification e-platform targeting healthy women in the general population can significantly increase knowledge as well as support decisions around breast cancer risk and assessment. Currently underway, Phase 2, called PERSPECTIVE, is seeking further content integration and broader implementation .

Sample Preparation for High-Throughput Urine Proteomics Using 96-Well Polyvinylidene Fluoride (PVDF) Membranes.

Proteomics analysis of urine samples allows for studying the impact of system perturbation. However, meaningful proteomics-based biomarker discovery projects often require the analysis of large patient cohorts with hundreds of samples to describe the biological variability. Thus, robust high-throughput sample processing methods are a prerequisite for clinical proteomics pipelines that minimize experimental bias due to individual sample processing methods. Herein we describe a high-throughput method for parallel 96-well plate-based processing of urine samples for subsequent LC/MS-based proteomic analyses. Protein digestion and subsequent sample processing steps are efficiently performed in 96-well polyvinylidene fluoride (PVDF) membrane plate allowing for the use of vacuum manifolds for rapid liquid transfer, and multichannel pipettes and/or liquid handing robots. In this chapter we make available a detailed step-by-step protocol for our 'MStern blotting' sample processing strategy applied to patient urine samples followed by mass spectrometry-based proteomics analysis. Subsequently, we provide an example application using minimal volume of urine samples (e.g. 150 µL) collected from children pre and post thoracotomy to identify the predominant sites of protein catabolism and aid in the design of therapies to ameliorate protein catabolism and breakdown during critical illness. Furthermore, we demonstrate how the systemic state is reflected in the urine as an easily obtainable, stable, and safe biofluid.