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1.
Machine learning-guided engineering of genetically encoded fluorescent calcium indicators.
Wait, SJ, Expòsit, M, Lin, S, Rappleye, M, Lee, JD, Colby, SA, Torp, L, Asencio, A, Smith, A, Regnier, M, et al
Nature computational science. 2024;(3):224-236
Abstract
Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which outperforms the tested sixth-, seventh- and eighth-generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient engineering of proteins for desired biophysical characteristics.
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Effects of ADHD and ADHD treatment on glycemic management in type 1 diabetes: A systematic review and meta-analysis of observational studies.
Zare Dehnavi, A, Elmitwalli, I, Alsharif, HOH, Shervin Razavi, A, Gumpel, TA, Smith, A, Weinstock, RS, Faraone, SV, Zhang-James, Y
Diabetes research and clinical practice. 2024;:111566
Abstract
AIMS: Studies suggested a higher prevalence of Attention-deficit/hyperactivity disorder (ADHD) in individuals with Type 1 Diabetes Mellitus (T1D). However, it is unclear how ADHD impacts glycemia and diabetes-related complications. This systematic review and meta-analysis aimed to investigate the effect of ADHD and ADHD medications on HbA1c and acute complications in T1D. METHODS A literature search was conducted in PubMed, EMBASE, CINAHL, Scopus, PsycINFO, CENTRAL, and Web of Science collections up to November 22, 2023. Seventeen studies were selected for the systematic review by independent reviewers, with twelve included in the meta-analysis. RESULTS Mean HbA1c levels were significantly higher in T1D individuals with ADHD compared to those without ADHD (MD = 0.60; 95 % CI: 0.41, 0.79; I2 = 90.1 %; p-value < 0.001). The rates of suboptimal HbA1c levels, hospitalization, diabetic ketoacidosis, and hypoglycemia were all substantially higher in T1D individuals with ADHD than those without ADHD. No difference was found in mean HbA1c between those who received ADHD treatment and those who did not (mean difference = -0.52; 95 % confidence interval: -1.16, 0.13; I2 = 78.6 %; p-value = 0.12). CONCLUSIONS ADHD is associated with higher HbA1c and increased acute diabetes-related complications. More research is needed to assess the effects of ADHD treatments on T1D management.
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Study protocol: peer delivered early intervention (Learning through Everyday Activities with Parents for Infants at risk of Cerebral Palsy: LEAP-CP) for First Nation Australian infants at high risk of cerebral palsy - an RCT study.
Benfer, K, Boyd, RN, Roe, Y, Fagan, R, Luke, C, Mick-Ramsamy, L, Whittingham, K, Novak, I, Bosanquet, M, McNamara, L, et al
BMJ open. 2023;(3):e059531
Abstract
INTRODUCTION Cerebral palsy (CP) is the most common childhood physical disability with rates approximately 50% higher in First Nations Australian children. This study aims to evaluate a culturally-adapted parent-delivered early intervention programme for First Nations Australian infants at high risk of CP (Learning through Everyday Activities with Parents for infants with CP; LEAP-CP). METHODS AND ANALYSIS This study is a randomised assessor masked controlled trial. Infants with birth/postnatal risk factors will be eligible for screening. Infants at high risk of CP ('absent fidgety' on General Movements Assessment, and/or 'suboptimal score' on the Hammersmith Infant Neurological Examination) aged 12-52 weeks corrected age will be recruited. Infants and their caregivers will be randomised to receive LEAP-CP (intervention) or health advice (comparator). LEAP-CP is a culturally-adapted programme of 30 home visits delivered by a peer trainer (First Nations Community Health Worker); and includes goal-directed active motor/cognitive strategies, CP learning games and caregiver educational modules. The control arm receives a monthly health advice visit, based on the Key Family Practices, WHO. All infants continue to receive standard (mainstream) Care as Usual. Dual child primary outcomes are Peabody Developmental Motor Scales-2 (PDMS-2) and Bayley Scales of Infant Development-III. The primary caregiver outcome is the Depression, Anxiety and Stress Scale. Secondary outcomes include function, goal attainment, vision, nutritional status and emotional availability. SAMPLE SIZE total of 86 children (43/group) will enable an effect size of 0.65 on the PDMS-2 to be detected (80% power, α=0.05; 10% attrition). ETHICS AND DISSEMINATION Ethics approval through Queensland ethics committees and Aboriginal Controlled Community Health Organisation Research Governance Groups, with families providing written informed consent. Findings will be disseminated with guidance from the Participatory Action Research, in collaboration with First Nations communities; peer-reviewed journal publications and national/international conference presentations. TRIAL REGISTRATION NUMBER ACTRN12619000969167p.
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Probiotic Supplementation for Promotion of Growth in Undernourished Children: A Systematic Review and Meta-Analysis.
Imdad, A, Pandit, NG, Ehrlich, JM, Catania, J, Zaman, M, Smith, A, Tanner-Smith, EE, Zackular, JP, Bhutta, ZA
Journal of pediatric gastroenterology and nutrition. 2023;(6):e84-e92
Abstract
OBJECTIVES Probiotic supplementation has been proposed as a therapeutic intervention to improve growth outcomes in children with undernutrition. The objective of this review is to synthesize the current evidence on probiotic supplementation for promotion of growth in undernourished children. METHODS We searched MEDLINE, Cochrane CENTRAL, CINAHL, Embase, LILACS, and Scopus for randomized controlled trials (RCTs) that administered probiotics or eligible comparators to undernourished children below 5 years of age. Our primary outcomes of interest were weight-for-age, height-for-age, and weight-for-height at the longest follow-up points reported. Random-effects meta-analysis was used to calculate standardized mean differences (SMD) for continuous outcomes and risk ratios for dichotomous outcomes. The Grading of Recommendations Assessment, Development and Evaluation criteria were used to assess certainty of the evidence. RESULTS Nine RCTs with 5295 children in total were included. Durations of treatment ranged from 1 month to 1 year. Pooled analyses from 7 studies showed that probiotics may have little to no effect on weight-for-age (SMD 0.05 standard deviation [SD], 95% CI: -0.04 to 0.13, n = 2115 children; low-certainty evidence) and height-for-age (SMD -0.04 SD, 95% CI: -0.14 to 0.07, n = 1357 children; low-certainty evidence). The evidence was very uncertain about the effect on weight-for-height. CONCLUSIONS Probiotics may have little to no effect on anthropometry in undernourished children, though there is considerable heterogeneity among the trials reviewed thus far. The interaction between gut microbiota and human nutrition is complex, and further research is needed to determine how the gut microbiome may contribute to undernutrition and how probiotics may affect growth in this vulnerable population.
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Importance of Ileum and Colon in Children with Short Bowel Syndrome.
Smith, A, Namjoshi, S, Kerner, JA, Dunn, JCY
Journal of pediatric surgery. 2023;(7):1258-1262
Abstract
BACKGROUND It is well known that small bowel length is a dominant prognostic indicator in patients with short bowel syndrome (SBS). The relative importance of jejunum, ileum, and colon is less well defined in children with SBS. Here we review the outcome of children with SBS with respect to the type of remnant intestine. METHODS A retrospective review of 51 children with SBS was conducted at a single institution. The duration of parenteral nutrition use was the main outcome variable. The length of the remaining intestine as well as the type of intestine were recorded for each patient. Kaplan-Meier analyses were conducted to compare the subgroups. RESULTS Children with greater than 10% expected small bowel length or more than 30 cm of small bowel achieved enteral autonomy faster than those with less. The presence of ileocecal valve enhanced the ability to wean from parenteral nutrition. The presence of ileum significantly enhanced the ability to wean from parenteral nutrition. Patients with the entire colon also achieved enteral autonomy sooner than those with partial colon. CONCLUSIONS The preservation of ileum and colon is important in patients with SBS. Approaches to preserve or lengthen ileum and colon may be beneficial for these patients. LEVEL OF EVIDENCE IV.
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Zinc supplementation for preventing mortality, morbidity, and growth failure in children aged 6 months to 12 years.
Imdad, A, Rogner, J, Sherwani, RN, Sidhu, J, Regan, A, Haykal, MR, Tsistinas, O, Smith, A, Chan, XHS, Mayo-Wilson, E, et al
The Cochrane database of systematic reviews. 2023;(3):CD009384
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Abstract
BACKGROUND Zinc deficiency is prevalent in low- and middle-income countries, and is considered a significant risk factor for morbidity, mortality, and linear growth failure. The effectiveness of preventive zinc supplementation in reducing prevalence of zinc deficiency needs to be assessed. OBJECTIVES To assess the effects of zinc supplementation for preventing mortality and morbidity, and for promoting growth, in children aged 6 months to 12 years. SEARCH METHODS A previous version of this review was published in 2014. In this update, we searched CENTRAL, MEDLINE, Embase, five other databases, and one trials register up to February 2022, together with reference checking and contact with study authors to identify additional studies. SELECTION CRITERIA Randomized controlled trials (RCTs) of preventive zinc supplementation in children aged 6 months to 12 years compared with no intervention, a placebo, or a waiting list control. We excluded hospitalized children and children with chronic diseases or conditions. We excluded food fortification or intake, sprinkles, and therapeutic interventions. DATA COLLECTION AND ANALYSIS Two review authors screened studies, extracted data, and assessed the risk of bias. We contacted study authors for missing information and used GRADE to assess the certainty of evidence. The primary outcomes of this review were all-cause mortality; and cause-specific mortality, due to all-cause diarrhea, lower respiratory tract infection (LRTI, including pneumonia), and malaria. We also collected information on a number of secondary outcomes, such as those related to diarrhea and LRTI morbidity, growth outcomes and serum levels of micronutrients, and adverse events. MAIN RESULTS We included 16 new studies in this review, resulting in a total of 96 RCTs with 219,584 eligible participants. The included studies were conducted in 34 countries; 87 of them in low- or middle-income countries. Most of the children included in this review were under five years of age. The intervention was delivered most commonly in the form of syrup as zinc sulfate, and the most common dose was between 10 mg and 15 mg daily. The median duration of follow-up was 26 weeks. We did not consider that the evidence for the key analyses of morbidity and mortality outcomes was affected by risk of bias. High-certainty evidence showed little to no difference in all-cause mortality with preventive zinc supplementation compared to no zinc (risk ratio (RR) 0.93, 95% confidence interval (CI) 0.84 to 1.03; 16 studies, 17 comparisons, 143,474 participants). Moderate-certainty evidence showed that preventive zinc supplementation compared to no zinc likely results in little to no difference in mortality due to all-cause diarrhea (RR 0.95, 95% CI 0.69 to 1.31; 4 studies, 132,321 participants); but probably reduces mortality due to LRTI (RR 0.86, 95% CI 0.64 to 1.15; 3 studies, 132,063 participants) and mortality due to malaria (RR 0.90, 95% CI 0.77 to 1.06; 2 studies, 42,818 participants); however, the confidence intervals around the summary estimates for these outcomes were wide, and we could not rule out a possibility of increased risk of mortality. Preventive zinc supplementation likely reduces the incidence of all-cause diarrhea (RR 0.91, 95% CI 0.90 to 0.93; 39 studies, 19,468 participants; moderate-certainty evidence) but results in little to no difference in morbidity due to LRTI (RR 1.01, 95% CI 0.95 to 1.08; 19 studies, 10,555 participants; high-certainty evidence) compared to no zinc. There was moderate-certainty evidence that preventive zinc supplementation likely leads to a slight increase in height (standardized mean difference (SMD) 0.12, 95% CI 0.09 to 0.14; 74 studies, 20,720 participants). Zinc supplementation was associated with an increase in the number of participants with at least one vomiting episode (RR 1.29, 95% CI 1.14 to 1.46; 5 studies, 35,192 participants; high-certainty evidence). We report a number of other outcomes, including the effect of zinc supplementation on weight and serum markers such as zinc, hemoglobin, iron, copper, etc. We also performed a number of subgroup analyses and there was a consistent finding for a number of outcomes that co-supplementation of zinc with iron decreased the beneficial effect of zinc. AUTHORS' CONCLUSIONS Even though we included 16 new studies in this update, the overall conclusions of the review remain unchanged. Zinc supplementation might help prevent episodes of diarrhea and improve growth slightly, particularly in children aged 6 months to 12 years of age. The benefits of preventive zinc supplementation may outweigh the harms in regions where the risk of zinc deficiency is relatively high.
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Curcumin, a dietary natural supplement, prolongs the action potential duration of KCNE1-D85N-induced pluripotent stem cell-derived cardiomyocytes.
Martinez, K, Smith, A, Ye, D, Zhou, W, Tester, DJ, Ackerman, MJ
Heart rhythm. 2023;(4):580-586
Abstract
BACKGROUND Curcumin, a polyphenolic dietary natural compound and active ingredient in turmeric, exerts antioxidant, anti-inflammatory, antidiabetic, anticancer, and antiarrhythmic properties. KCNE1-D85N, present in ∼1% of white, is a common, potentially proarrhythmic variant that predisposes individuals to drug-induced QT prolongation under certain conditions. OBJECTIVE The purpose of this article was to test the hypothesis that curcumin might cause action potential duration (APD) prolongation in KCNE1-D85N-derived human-induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). METHODS Gene-edited/variant-corrected isogenic control and patient-specific KCNE1-D85N-containing iPSC-CMs were generated previously. Voltage-sensing dye, multielectrode array (MEA), and whole-cell patch clamp technique were used to measure APD without and with 4-hour incubation with 10 nM curcumin. RESULTS KCNE1-D85N-derived iPSC-CMs demonstrated significant APD prolongation with treatment of 10 nM curcumin. Using voltage-sensing dye, action potential duration at 90% repolarization (APD90) was 578 ± 7 ms (n = 39) at baseline and was prolonged to 658 ± 13 ms (n = 35) with curcumin incubation (P < .0001). Using MEA, APD90 at baseline was 237 ± 6 ms (n = 24) compared with 280 ± 6 ms (n = 12) with curcumin incubation (P = .0002). The whole-cell patch clamp technique confirmed these results, with APD90 being 544 ± 37 ms at baseline and 664 ± 40 ms with treatment of curcumin (P < .005). However, APD from isogenic control iPSC-CMs remained unchanged with curcumin treatment. CONCLUSION This study provides pharmacological and functional evidence to suggest that curcumin, a dietary natural supplement, might cause APD prolongation in patients with common, potentially proarrhythmic functional variants such as KCNE1-D85N. Whether this supplement is potentially dangerous for the Caucasian subpopulation that has this variant warrants further investigation.
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Diabetes remission and relapse following an intensive metabolic intervention combining insulin glargine/lixisenatide, metformin and lifestyle approaches: Results of a randomised controlled trial.
McInnes, N, Hall, S, Lochnan, HA, Harris, SB, Punthakee, Z, Sigal, RJ, Hramiak, I, Azharuddin, M, Liutkus, JF, Yale, JF, et al
Diabetes, obesity & metabolism. 2023;(11):3347-3355
Abstract
AIM: Non-surgical options for inducing type 2 diabetes remission are limited. We examined whether remission can be achieved by combining lifestyle approaches and short-term intensive glucose-lowering therapy. METHODS In this trial, 160 patients with type 2 diabetes on none to two diabetes medications other than insulin were randomised to (a) an intervention comprising lifestyle approaches, insulin glargine/lixisenatide and metformin, or (b) standard care. Participants with glycated haemoglobin (HbA1c) <7.3% (56 mmol/mol) at 12 weeks were asked to stop diabetes medications and were followed for an additional 52 weeks. The primary outcome was diabetes relapse defined as HbA1c ≥6.5% (48 mmol/mol) at 24 weeks or thereafter, capillary glucose ≥10 mmol/L on ≥50% of readings, or use of diabetes medications, analysed as time-to-event. Main secondary outcomes included complete or partial diabetes remission at 24, 36, 48 and 64 weeks defined as HbA1c <6.5% (48 mmol/mol) off diabetes medications since 12 weeks after randomisation. A hierarchical testing strategy was applied. RESULTS The intervention significantly reduced the hazard of diabetes relapse by 43% (adjusted hazard ratio 0.57, 95% confidence interval 0.40-0.81; p = .002). Complete or partial diabetes remission was achieved in 30 (38.0%) intervention group participants versus 16 (19.8%) controls at 24 weeks and 25 (31.6%) versus 14 (17.3%) at 36 weeks [relative risk 1.92 (95% confidence interval 1.14-3.24) and 1.83 (1.03-3.26), respectively]. The relative risk of diabetes remission in the intervention versus control group was 1.88 (1.00-3.53) at 48 weeks and 2.05 (0.98-4.29) at 64 weeks. CONCLUSIONS A 12-week intensive intervention comprising insulin glargine/lixisenatide, metformin and lifestyle approaches can induce remission of diabetes.
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SGLT2 inhibitors reduce sudden cardiac death risk in heart failure: Meta-analysis of randomized clinical trials.
Oates, CP, Santos-Gallego, CG, Smith, A, Basyal, B, Moss, N, Kawamura, I, Musikantow, DR, Turagam, MK, Miller, MA, Whang, W, et al
Journal of cardiovascular electrophysiology. 2023;(5):1277-1285
Abstract
INTRODUCTION Multiple randomized controlled trials have demonstrated sodium-glucose cotransporter-2 inhibitors (SGLT2i) decrease the composite endpoint of cardiovascular death or heart failure hospitalizations in all heart failure patients. It is uncertain whether SGLT2i impacts the risk of sudden cardiac death in patients with heart failure. METHODS A comprehensive search was performed to identify relevant data published before August 28, 2022. Trials were included if: (1) all patients had clinical heart failure (2) SGLT2i and placebo were compared (3) all patients received conventional medical therapy and (4) reported outcomes of interest (sudden cardiac death [SCD], ventricular arrhythmias, atrial arrhythmias). RESULTS SCD was reported in seven of the eleven trials meeting selection criteria: 10 796 patients received SGLT2i and 10 796 received placebo. SGLT2i therapy was associated with a significant reduction in the risk of SCD (risk ratios [RR]: 0.68; 95% confidence intervals [CI]: 0.48-0.95; p = .03; I2 = 0%). Absent dedicated rhythm monitoring, there were no significant differences in the incidence of sustained ventricular arrhythmias not associated with SCD (RR: 1.03; 95% CI: 0.83-1.29; p = .77; I2 = 0%) or atrial arrhythmias (RR: 0.91; 95% CI: 0.77-1.09; p = .31; I2 = 29%) between patients receiving an SGLT2i versus placebo. CONCLUSION SGLT2i therapy is associated with a reduced risk of SCD in patients with heart failure receiving contemporary medical therapy. Prospective trials are needed to determine the long-term impact of SGLT2i therapy on atrial and ventricular arrhythmias.
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Personalised recommendations for hospitalised patients with Acute Kidney Injury using a Kidney Action Team (KAT-AKI): protocol and early data of a randomised controlled trial.
Aklilu, AM, O'Connor, KD, Martin, M, Yamamoto, Y, Coronel-Moreno, C, Shvets, K, Jones, C, Kadhim, B, Corona-Villalobos, CP, Baker, ML, et al
BMJ open. 2023;(4):e071968
Abstract
INTRODUCTION Although studies have examined the utility of clinical decision support tools in improving acute kidney injury (AKI) outcomes, no study has evaluated the effect of real-time, personalised AKI recommendations. This study aims to assess the impact of individualised AKI-specific recommendations delivered by trained clinicians and pharmacists immediately after AKI detection in hospitalised patients. METHODS AND ANALYSIS KAT-AKI is a multicentre randomised investigator-blinded trial being conducted across eight hospitals at two major US hospital systems planning to enrol 4000 patients over 3 years (between 1 November 2021 and 1 November 2024). A real-time electronic AKI alert system informs a dedicated team composed of a physician and pharmacist who independently review the chart in real time, screen for eligibility and provide combined recommendations across the following domains: diagnostics, volume, potassium, acid-base and medications. Recommendations are delivered to the primary team in the alert arm or logged for future analysis in the usual care arm. The planned primary outcome is a composite of AKI progression, dialysis and mortality within 14 days from randomisation. A key secondary outcome is the percentage of recommendations implemented by the primary team within 24 hours from randomisation. The study has enrolled 500 individuals over 8.5 months. Two-thirds were on a medical floor at the time of the alert and 17.8% were in an intensive care unit. Virtually all participants were recommended for at least one diagnostic intervention. More than half (51.6%) had recommendations to discontinue or dose-adjust a medication. The median time from AKI alert to randomisation was 28 (IQR 15.8-51.5) min. ETHICS AND DISSEMINATION The study was approved by the ethics committee of each study site (Yale University and Johns Hopkins institutional review board (IRB) and a central IRB (BRANY, Biomedical Research Alliance of New York). We are committed to open dissemination of the data through clinicaltrials.gov and sharing of data on an open repository as well as publication in a peer-reviewed journal on completion. TRIAL REGISTRATION NUMBER NCT04040296.