Perturbation-Specific Transcriptional Mapping for unbiased target elucidation of antibiotics

The rising prevalence of antibiotic resistance threatens human health. While more sophisticated strategies for antibiotic discovery are being developed, target elucidation of new chemical entities remains challenging. In the post-genomic era, expression profiling can play an important role in mechanism-of-action (MOA) prediction by reporting on the cellular response to perturbation. However, the broad application of transcriptomics has yet to fulfill its promise of transforming target elucidation due to challenges in identifying the most relevant, direct responses to target inhibition. We developed an unbiased strategy for MOA prediction, called Perturbation-Specific Transcriptional Mapping (PerSpecTM), in which large-throughput expression profiling of wildtype or hypomorphic mutants, depleted for essential targets, enables a computational strategy to address this challenge. We applied PerSpecTM to perform reference-based MOA prediction based on the principle that similar perturbations, whether small molecule or genetic, will elicit similar transcriptional responses. Using this approach, we elucidated the MOAs of three new molecules with activity against Pseudomonas aeruginosa by mapping their expression profiles to those of a reference set of antimicrobial compounds with known MOAs. We also show that transcriptional responses to small molecule inhibition maps to those resulting from genetic depletion of essential targets by CRISPRi by PerSpecTM, demonstrating proof-of-concept that correlations between expression profiles of small molecule and genetic perturbations can facilitate MOA prediction when no chemical entities exist to serve as a reference. Empowered by PerSpecTM, this work lays the foundation for an unbiased, readily scalable, systematic reference-based strategy for MOA elucidation that could transform antibiotic discovery efforts.

Significance Statement

New antibiotics are critically needed in the face of increasing antibiotic resistance. However, mechanism-of-action (MOA) elucidation remains challenging and imposes a major bottleneck in antibiotic discovery and development. Building on the principle that molecules with similar MOAs elicit similar transcriptional responses, we have developed a highly scalable strategy for MOA prediction in the important bacterial pathogen Pseudomonas aeruginosa based on correlations between the expression profiles of new molecules and known perturbations, either small molecule inhibition by known antibiotics or transcriptional repression of essential targets by CRISPRi. By rapidly assigning MOAs to three new molecules with anti-pseudomonal activity, we provide proof-of-concept for a rapid, comprehensive, systematic, reference-based approach to MOA prediction with the potential to transform antibiotic discovery efforts.

Deworming and micronutrient status by community open defecation prevalence: An observational study using nationally representative data from India, 2016-2018

BACKGROUND

Micronutrient deficiencies are widespread in India. Soil-transmitted helminth (STH) infections are acquired by interaction with soil and water contaminated by human feces and lead to blood loss and poor micronutrient absorption. The current recommendation for control of STH-related morbidity is targeted deworming, yet little is known about the effectiveness of deworming on micronutrient status in varying sanitation contexts. Ranging between 1% and 40% prevalence across Indian states, open defecation (OD) remains high despite India's investments at elimination by promoting community-wide sanitation. This variation provides an opportunity to study the relationship between deworming, micronutrient status, and OD at-scale.

METHODS AND FINDINGS

Cross-sectional datasets that were representative for India were obtained the Comprehensive National Nutrition Survey in 2016 to 2018 (n = 105,060 individuals aged 1 to 19 years). Consumption of deworming medication was described by age and community OD level. Logistic regression models were used to examine the relationship between deworming, cluster OD, and their interactions, with anemia and micronutrient deficiencies (iron, zinc, vitamin A, folate, and vitamin B12), controlling for age, sex, wealth, diet, and seasonality. These regression models further allowed us to identify a minimum OD rate after which deworming becomes ineffective. In sensitivity analyses, the association between deworming and deficiencies were tested in subsamples of communities classified into 3 OD levels based on statistical tertiles: OD free (0% of households in the community practicing OD), moderate OD (>0% and <30%), or high OD (at least 30%). Average deworming coverage and OD prevalence in the sample were 43.4% [IQR 26.0, 59.0] and 19.1% [IQR 0, 28.5], respectively. Controlling for other determinants of nutritional status, adolescents living in communities with higher OD levels had lower coverage of deworming and higher prevalence of anemia, zinc, vitamin A, and B12 deficiencies. Compared to those who were not dewormed, dewormed children and adolescents had lower odds of anemia (adjusted odds ratio 0.72, (95% CI [0.67, 0.78], p < 0.001) and deficiencies of iron 0.78, (95% CI [0.74, 0.82], p < 0.001) and folate 0.69, (95% CI [0.64,0.74], p<0.001)) in OD free communities. These protective effects remained significant for anemia but diminished for other micronutrient deficiencies in communities with moderate or high OD. Analysis of community OD indicated a threshold range of 30% to 60%, above which targeted deworming was no longer significantly associated with lower anemia, iron, and folate deficiency. The primary limitations of the study included potential for omitted variables bias and inability to capture longitudinal effects.

CONCLUSIONS

Moderate to high rates of OD significantly modify the association between deworming and micronutrient status in India. Public health policy could involve sequencing interventions, with focus on improving deworming coverage in communities that have achieved minimum thresholds of OD and re- triggering sanitation interventions in high OD communities prior to deworming days, ensuring high coverage for both. The efficacy of micronutrient supplementation as a complementary strategy to improve nutritional outcomes alongside deworming and OD elimination in this age group needs further study.

Utilization of Integrated Child Development Services (ICDS) and its linkages with undernutrition in India

The Integrated Child Development Services (ICDS) programme has been the central focus of the POSHAN Abhiyaan to combat maternal and child malnutrition under the national nutrition mission in India. This paper examined the linkages between utilization of ICDS and underweight among children aged 6-59 months. The study utilized data from two recent rounds of the National Family Health Survey (NFHS-4 [2015-2016] and NFHS-5 [2019-2021]). Descriptive analyses were used to assess the change in utilization of ICDS and the prevalence of underweight at the national and state levels. Multivariable logistic regressions were performed to examine factors associated with the utilization of ICDS and underweight. Linkages between utilization of ICDS and underweight were examined using the difference-in-differences (DID) approach. Utilization of ICDS increased from 58% in 2015-2016 to 71% in 2019-2021. The prevalence of underweight decreased from 37% to 32% in the same period. Changes in ICDS utilization and underweight prevalence varied considerably across states, socioeconomic and demographic characteristics. Results from decomposition of DID models suggest that improvements in ICDS explained 9%-12% of the observed reduction in underweight children between 2016 and 2021, suggesting that ICDS made a modest but meaningful contribution in addressing undernutrition among children aged 6-59 months in this period.

Preconception Micronutrient Supplementation Affects Maternal BMI and Body Composition Postpartum: A Randomized Controlled Trial in Vietnam

BACKGROUND

Although there is growing evidence on the role of preconception nutrition for birth outcomes, limited evidence exists for its effects on maternal health.

OBJECTIVES

This study evaluates the impact of preconception micronutrient supplementation on maternal BMI (kg/m2) and body composition at 6 to 7 y postpartum (PP).

METHODS

We followed females who participated in a randomized controlled trial of preconception supplementation in Vietnam and delivered live offspring (n = 1599). Females received weekly supplements containing either 2800 μg folic acid (FA) only, 60 mg iron and 2800 μg FA (IFA), or multiple micronutrients (MMs) (15 micronutrients including IFA) from baseline until conception followed by daily prenatal IFA supplements until delivery. Height, weight, mid-upper arm circumference, triceps skinfold, and waist-hip circumference were measured at recruitment and at 1, 2, and 6 to 7 y PP. Body fat was assessed using bioelectric impedance at 6 to 7 y PP (n = 867). Group comparisons were made using analysis of variance or chi-square tests and general linear models for adjusted models.

RESULTS

At 6 to 7 y PP, we found significant differences (P < 0.05) by treatment group for mean percent fat (MM: 29.2%; IFA: 27.6%; FA: 27.8%), absolute fat mass (MM: 15.1 kg; IFA: 14.0 kg; FA: 14.3 kg), and prevalence of underweight based on BMI < 18.5 (MM: 5.8%; IFA: 10.3%; FA: 14.3%). Mean BMI and triceps skinfold thickness were higher in the MM group, but these differences were not statistically significant; the differences in absolute fat mass were also attenuated after controlling for body weight. No differences were observed for fat-free mass, prevalence of overweight (BMI >23), or other anthropometric measurements.

CONCLUSIONS

Preconception MM supplementation was associated with lower prevalence of underweight and higher percent fat when compared with IFA and/or FA only. Preconception micronutrient interventions may have long-term effects on maternal health and merit further examination. This trial was registered at clinicaltrials.gov as NCT01665378.

"Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS"

The surge of antimicrobial resistance threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa , a highly resistant gram-negative pathogen. The asymmetric outer membrane (OM) of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic accumulation, thus making antibiotic discovery challenging. We adapted PROSPECT 1 , a target-based, whole-cell screening strategy, to discover small molecule probes that kill P. aeruginosa mutants depleted for essential proteins localized at the OM. We identified BRD1401, a small molecule that has specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Genetic and chemical biological studies identified that BRD1401 acts by targeting the OM β-barrel protein OprH to disrupt its interaction with LPS and increase membrane fluidity. Studies with BRD1401 also revealed an interaction between OprL and OprH, directly linking the OM with peptidoglycan. Thus, a whole-cell, multiplexed screen can identify species-specific chemical probes to reveal novel pathogen biology.

Utilizing surface plasmon resonance as a novel method for monitoring in-vitro P-glycoprotein efflux

P-glycoprotein (Pgp) is known for its dichotomous roles as both a safeguarding efflux transporter against xenobiotics and as a catalyst for multidrug resistance. Given the susceptibility of numerous therapeutic compounds to Pgp-mediated resistance, compliance with Food and Drug Administration (FDA) guidelines mandates an in-depth in vitro transport assay during drug development. This study introduces an innovative transport assay that aligns with these regulatory imperatives but also addresses limitations in the currently established techniques. Using Pgp-reconstituted liposomes and employing surface plasmon resonance (SPR), this study developed a distinct method of measuring the relative transport rates of Pgp substrates in a controlled microenvironment. The Pgp substrates selected for this study-quinidine, methadone, and desipramine-resulted in transport ratios that corroborate with trends previously observed. To assess the kinetics of Pgp-mediated transport, the results were analyzed by fitting the data to both currently proposed Pgp substrate translocation models-the vacuum cleaner and flippase models. While the resulting kinetic analysis in this study lends support predominantly to the vacuum cleaner model, this study most notably developed a novel method of assessing Pgp-mediated transport rates and real-time kinetics using surface plasmon resonance.

The relationships between optimal infant feeding practices and child development and attained height at age 2 years and 6-7 years

Limited evidence exists on the long-term effects of early feeding practices on child growth and development. We examined the relationships between infant feeding practices and child height and development at ages 2 and 6-7 years. We studied 885 mother-child dyads from a randomized controlled trial of preconception supplementation in Vietnam. Early initiation of breastfeeding (EIBF), exclusive breastfeeding (EBF), breastfeeding (BF) duration and minimum dietary diversity (MDD) were assessed using World Health Organization (WHO) guidelines. Child development was assessed by the Bayley Scales of Infant Development-III at 2 years and the Wechsler Intelligence Scale for Children® - IV at 6-7 years. Child height-for-age z-score (HAZ) was calculated from child height and age. Multivariable regression and structural equation models were used in analyses that controlled for confounding. EIBF and EBF at 6 months occurred in 52% and 62% of children, respectively. Mean breastfeeding duration was 18 months and 83% achieved MDD at 1 year. EIBF was associated with motor (β = 0.13, 95% confidence interval [CI]: 0.00, 0.28) and cognitive development at 2 years (β = 0.12, 95% CI: -0.01, 0.26), which in turn were positively associated with cognitive development at 6-7 years. EBF was directly associated with development at 6-7 years (β = 0.21, 95% CI:0.08, 0.34) whereas motor and cognitive development at 2 years explained 41%-75% of the relationship between EIBF and development at 6-7 years. HAZ at 2 years also mediated 70% of the association between MDD at 1 year and HAZ at 6-7 years. BF duration was not associated with child development and HAZ. Early infant feeding practices, especially EIBF and EBF, have important long-term implications for optimizing child linear growth and cognition as they begin school.

Structure and Elasticity of Mitochondrial Membranes: A Molecular Dynamics Simulation Study

Mitochondria are known as the powerhouse of the cell because they produce energy in the form of adenosine triphosphate. They also have other crucial functions such as regulating apoptosis, calcium homeostasis, and reactive oxygen species production. To perform these diverse functions, mitochondria adopt specific structures and frequently undergo dynamic shape changes, indicating that their mechanical properties play an essential role in their functions. To gain a detailed understanding at the molecular level of the structure and mechanical properties of mitochondria, we carry out atomistic molecular dynamics simulations for three inner mitochondrial membranes and three outer mitochondrial membrane models. These models take into account variations in cardiolipin and cholesterol concentrations as well as the symmetry/asymmetry between the two leaflets. Our simulations allow us to calculate various structural quantities and the bending, twisting, and tilting elastic moduli of the membrane models. Our results indicate that the structures of the inner and outer mitochondrial membranes are quite similar and do not depend much on the variation in lipid compositions. However, the bending modulus of the membranes increases with increasing concentrations of cardiolipin or cholesterol but decreases with a membrane asymmetry. Notably, we found that the dipole potential of the membrane increases with an increasing cardiolipin concentration. Finally, possible roles of cardiolipin in regulating ion and proton currents and maintaining the cristate are discussed in some details.

Recent Computational Advances Regarding Amyloid-β and Tau Membrane Interactions in Alzheimer's Disease

The interactions of amyloid proteins with membranes have been subject to many experimental and computational studies, as these interactions contribute in part to neurodegenerative diseases. In this review, we report on recent simulations that have focused on the adsorption and insertion modes of amyloid-β and tau proteins in membranes. The atomistic-resolution characterization of the conformational changes of these amyloid proteins upon lipid cell membrane and free lipid interactions is of interest to rationally design drugs targeting transient oligomers in Alzheimer's disease.

Strengthening Nutrition Interventions during Antenatal Care Improved Maternal Dietary Diversity and Child Feeding Practices in Urban Bangladesh: Results of a Quasi-Experimental Evaluation Study

BACKGROUND

Bangladesh is urbanizing rapidly, facing challenges of malnutrition, low coverage and poor quality of urban nutrition services.

OBJECTIVES

We assessed the effect of integrating maternal, infant, and young child nutrition interventions, delivered at urban Maternal Neonatal and Child Health facilities, on maternal dietary diversity, iron and folic acid (IFA) and calcium consumption, and child feeding practices.

METHODS

We used a quasi-experimental design with a nonrandom assignment of 20 health care facilities in Dhaka to intensive and standard service arms. We conducted facility-based observations and community-based surveys at baseline (2020) and endline (2022) (n = 2455 observations and surveys with 1678 pregnant women [PW] or recently delivered women [RDW] at endline). We derived difference-in-difference (DID) estimates, adjusted for characteristics that differed at baseline or endline, and accounted for clustering.

RESULTS

Exposure to antenatal care (ANC) was similar in both arms: two-thirds of RDW received ANC during the first trimester and three-fourths received ≥4 ANC checkups. Compared to the standard arm, a higher proportion of PW in the intensive arm received counseling on dietary diversity (DID: 45 percentage points [pp]), and a higher proportion of RDW received IFA (25 pp) and calcium supplementation (19 pp), showed adequate weight gain (44 pp), and recorded appropriate child feeding (27 pp). Improvements were greater in the intensive than the standard arm for the number of food groups consumed (DID: 1.1 food groups) and minimum dietary diversity (23 pp); no effect was observed for IFA and calcium consumption during pregnancy. However, effects were observed for early initiation of (20 pp) and exclusive breastfeeding (45 pp), introduction of solid or semisolid foods (28 pp), and egg and/or flesh food consumption (33 pp) among children. Minimum dietary diversity and acceptable diet remained low in both arms.

CONCLUSIONS

Intensifying nutrition in government-aligned health care services delivered by experienced nongovernmental organization-run facilities is a feasible model to address the urban health gap, nutrition services coverage, and improve practices. The trial was registered at clinicaltrials.gov as NCT03882268.

Concurrent Undernutrition and Overnutrition within Indian Families between 2006 and 2021

Background

The double burden of malnutrition (DBM), characterized by concurrent undernutrition and overnutrition, is a growing global concern. Families share resources and eating behaviors and programs often target households, yet evidence of the DBM at the family level is scarce.

Objectives

This study examined trends and inequality in the intrahousehold DBM in India between 2006 and 2021.

Methods

Data were from 3 waves of India's National Family Health Survey (NFHS 2006, 2016, and 2021). We examined 3 types of household member (with children aged <5 y) combinations: mother-child (N = 328,039 across 3 waves), father-child, and parent (mother and father)-child (N = 47,139 for each pair). The DBM was defined as one or more individuals with undernutrition (either wasting or stunting in children or underweight in adults) and one or more overweight individuals within the same household. DBM was examined over time, at national and subnational levels, and by residence and wealth.

Results

Nearly all DBM was in the form of an overweight parent and an undernourished weight or stunted child. The prevalence of parent-child DBM increased from 15% in 2006 to 26% in 2021. Father-child pairs experienced the most rapid DBM increase, from 12% in 2006 to 22% in 2021, an 83% increase, driven by increasing overweight among men. In 2021, the DBM was highest in North-Eastern and Southern states, and among relatively rich households from urban areas. The increase in the DBM was faster in rural areas and among poor households compared with that in urban areas and rich households. Urban-rural and rich-poor inequalities in the DBM have decreased over time.

Conclusions

The intrahousehold DBM has increased over time, affecting 1 in 4 households in India in 2021. Family-based interventions that can simultaneously address child underweight and parent overweight are required to address India's increasing intrahousehold DBM.

Opportunities and barriers for maternal nutrition behavior change: an in-depth qualitative analysis of pregnant women and their families in Uttar Pradesh, India

Background

Maternal undernutrition during pregnancy remains a critical public health issue in India. While evidence-based interventions exist, poor program implementation and limited uptake of behavior change interventions make addressing undernutrition complex. To address this challenge, Alive & Thrive implemented interventions to strengthen interpersonal counseling, micronutrient supplement provision, and community mobilization through the government antenatal care (ANC) platform in Uttar Pradesh, India.

Objective

This qualitative study aimed to: (1) examine pregnant women's experiences of key nutrition-related behaviors (ANC attendance, consuming a diverse diet, supplement intake, weight gain monitoring, and breastfeeding intentions); (2) examine the influence of family members on these behaviors; and (3) identify key facilitators and barriers that affect behavioral adoption.

Methods

We conducted a qualitative study with in-depth interviews with 24 pregnant women, 13 husbands, and 15 mothers-in-law (MIL). We analyzed data through a thematic approach using the Capability-Opportunity-Motivation-Behavior (COM-B) framework.

Results

For ANC checkups and maternal weight gain monitoring, key facilitators were frontline worker home visits, convenient transportation, and family support, while the primary barrier was low motivation and lack understanding of the importance of ANC checkups. For dietary diversity, there was high reported capability (knowledge related to the key behavior) and most family members were aware of key recommendations; however, structural opportunity barriers (financial strain, lack of food availability and accessibility) prevented behavioral change. Opportunity ranked high for iron and folic acid supplement (IFA) intake, but was not consistently consumed due to side effects. Conversely, lack of supply was the largest barrier for calcium supplement intake. For breastfeeding, there was low overall capability and several participants described receiving inaccurate counseling messages.

Conclusion

Key drivers of maternal nutrition behavior adoption were indicator specific and varied across the capability-opportunity-motivation behavior change spectrum. Findings from this study can help to strengthen future program effectiveness by identifying specific areas of program improvement.

Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations

As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.

Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

Structure and elasticity of healthy and Alzheimer's disease cell membranes revealed by molecular dynamics simulations

Interactions of amyloid-β (Aβ) peptides with neuronal membrane are associated with the development of Alzheimer's disease (AD). Ganglioside monosialotetrahexosylganglioside (GM1) lipids have been shown to form clusters that induce the structural conversion of Aβ and promote the incorporation of Aβ into the membrane via the membrane surface electrical potential. Prior to the onset of AD symptoms, GM1 clusters may not have formed but the concentration of GM1 may have already changed, and our question is whether this early concentration modification affects the structure and mechanical properties of the membrane. Using one model for healthy cell membranes and three models for AD cell membranes, we carry out 2 µs all-atom molecular dynamics simulations for each model to compare the structure and elasticity of the two membrane types. The simulations show that at the physiological concentration, 1%-3%, GM1 does not form clusters. The reduction of the GM1 lipid does not significantly alter the area per lipid, the membrane thickness, and the lipid order parameters of the AD membranes. However, the dipole potential, the bending, and twist moduli are decreased for the AD membranes. We suggest that these changes in the AD membranes are factors that could trigger the interaction and incorporation of Aβ to the membranes. Finally, we show that changes in the sphingomyelin lipid concentrations do not affect the membrane structure and elasticity.

Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers

Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and simulations on Aβ42 monomer point to random coil conformations with either transient helical or β-strand content. Our current conformational description of small Aβ42 oligomers is funneled toward amorphous aggregates with some β-sheet content and rare high energy states with well-ordered assemblies of β-sheets. In this study, we emphasize another view based on metastable α-helix bundle oligomers spanning the C-terminal residues, which are predicted by the machine-learning AlphaFold2 method and supported indirectly by low-resolution experimental data on many amyloid polypeptides. This finding has consequences in developing novel chemical tools and to design potential therapies to reduce aggregation and toxicity.

An S-Shaped Aβ42 Cross-β Hexamer Embedded into a Lipid Bilayer Reveals Membrane Disruption and Permeability

The interactions of amyloid oligomers with membranes are known to contribute to cellular toxicity. Numerous in vitro experimental studies reported on the insertion of oligomers of different sizes that can induce cell membrane disruption, extract lipids, and form ion-permeable transmembrane pores. The current repertoire of amyloid-beta (Aβ) membrane-inserted folds that was subject to high-resolution structure NMR spectroscopy and computer simulations is devoid of any cross-β fibrillar structure. In this study, we explored the dynamics of an S-shaped Aβ42 cross-β hexamer model inserted into a lipid bilayer membrane by two atomistic molecular dynamics simulations. The initial model is characterized by the hydrophobic residues at the central hydrophobic core (residues 17-21, CHC) and the C-terminus (residues 30-42) embedded into the membrane. We observed major structural secondary, tertiary, and quaternary rearrangements leading to two distinct species, hexamer and two trimers, accompanied by membrane disruption and water permeation. The simulations show that some configurations, but not the majority, have the CHC and C-terminus hydrophobic residues exposed to the solvent. Overall, our computational results offer new perspectives to understand the relationship between Aβ42 assemblies and membrane permeability.

Assessing the hidden burden and costs of COVID-19 pandemic in South Asia: Implications for health and well-being of women, children and adolescents

The COVID-19 pandemic has disproportionately affected vulnerable populations. With its intensity expected to be cyclical over the foreseeable future, and much of the impact estimates still modeled, it is imperative that we accurately assess the impact to date, to help with the process of targeted rebuilding of services. We collected data from administrative health information systems in six South Asian countries (Afghanistan, Bangladesh, Nepal, India, Pakistan and Sri Lanka), to determine essential health services coverage disruptions between January-December 2020, and January-June 2021, compared to the same calendar months in 2019, and estimated the impact of this disruption on maternal and child mortality using the Lives Saved Tool. We also modelled impact of prolonged school closures on continued enrollment, as well as potential sequelae for the cohort of girls who have likely dropped out. Coverage of key maternal and child health interventions, including antenatal care and immunizations, decreased by up to 60%, with the largest disruptions observed between April and June 2020. This was followed by a period of recovery from July 2020 to March 2021, but a reversal of most of these gains in April/May 2021, likely due to the delta variant-fueled surge in South Asia at the same time. We estimated that disruption of essential health services between January 2020 and June 2021 potentially resulted in an additional 19,000 maternal and 317,000 child deaths, an increase of 19% and 13% respectively, compared to 2019. Extended school closures likely resulted in 9 million adolescents dropping out permanently, with 40% likely being from poorest households, resulting in decreased lifetime earnings. A projected increase in early marriages for girls who dropped out could result in an additional 500,000 adolescent pregnancies, 153,000 low birthweight births, and 27,000 additional children becoming stunted by age two years. To date, the increase in maternal and child mortality due to health services disruption has likely exceeded the overall number of COVID-19 deaths in South Asia. The indirect effects of the pandemic were disproportionately borne by the most vulnerable populations, and effects are likely to be long-lasting, permanent and in some cases inter-generational, unless policies aimed at alleviating these impacts are instituted at scale and targeted to reach the poorest of the poor. There are also implications for future pandemic preparedness.

Insights into the Mixture of Aβ24 and Aβ42 Peptides from Atomistic Simulations

Amyloid-β (Aβ) oligomers play a central role in Alzheimer's disease (AD). Plaques of AD patients consist of Aβ40 and Aβ42 peptides and truncated Aβ peptides. The Aβ24 peptide, identified in human AD brains, was found to impair Aβ42 clearance through the brain-blood barrier. The Aβ24 peptide was also shown to reduce Aβ42 aggregation kinetics in pure buffer, but the underlying mechanism is unknown at atomistic level. In this study, we explored the conformational ensemble of the equimolar mixture of Aβ24 and Aβ42 by replica exchange molecular dynamics simulations and compared it to our previous results on the pure Aβ42 dimer. Our simulations demonstrate that the truncation at residue 24 changes the secondary, tertiary, and quaternary structures of the dimer, offering an explanation of the slower aggregation kinetics of the mixture.

Self-Assembly of Amyloid-Beta (Aβ) Peptides from Solution to Near In Vivo Conditions

Understanding the atomistic resolution changes during the self-assembly of amyloid peptides or proteins is important to develop compounds or conditions to alter the aggregation pathways and suppress the toxicity and potentially aid in the development of drugs. However, the complexity of protein aggregation and the transient order/disorder of oligomers along the pathways to fibril are very challenging. In this Perspective, we discuss computational studies of amyloid polypeptides carried out under various conditions, including conditions closely mimicking in vivo and point out the challenges in obtaining physiologically relevant results, focusing mainly on the amyloid-beta Aβ peptides.

Molecular dynamics simulation of cancer cell membrane perforated by shockwave induced bubble collapse

It has been widely accepted that cancer cells are softer than their normal counterparts. This motivates us to propose, as a proof-of-concept, a method for the efficient delivery of therapeutic agents into cancer cells, while normal cells are less affected. The basic idea of this method is to use a water jet generated by the collapse of the bubble under shockwaves to perforate pores in the cell membrane. Given a combination of shockwave and bubble parameters, the cancer membrane is more susceptible to bending, stretching, and perforating than the normal membrane because the bending modulus of the cancer cell membrane is smaller than that of the normal cell membrane. Therefore, the therapeutic agent delivery into cancer cells is easier than in normal cells. Adopting two well-studied models of the normal and cancer membranes, we perform shockwave induced bubble collapse molecular dynamics simulations to investigate the difference in the response of two membranes over a range of shockwave impulse 15-30 mPa s and bubble diameter 4-10 nm. The simulation shows that the presence of bubbles is essential for generating a water jet, which is required for perforation; otherwise, pores are not formed. Given a set of shockwave impulse and bubble parameters, the pore area in the cancer membrane is always larger than that in the normal membrane. However, a too strong shockwave and/or too large bubble results in too fast disruption of membranes, and pore areas are similar between two membrane types. The pore closure time in the cancer membrane is slower than that in the normal membrane. The implications of our results for applications in real cells are discussed in some details. Our simulation may be useful for encouraging future experimental work on novel approaches for cancer treatment.

Measuring adherence, acceptability and likability of an artificial-intelligence-based, gamified phone application to improve the quality of dietary choices of adolescents in Ghana and Vietnam: Protocol of a randomized controlled pilot test

Unhealthy diets are a critical global concern while dietary measure methods are time consuming and expensive. There is limited evidence that phone-based interventions can improve nutrition data collection and dietary quality, especially for adolescents in developing countries. We developed an artificial-intelligence-based phone application called Food Recognition Assistance and Nudging Insights (FRANI) to address these problems. FRANI can recognize foods in images, track food consumption, display statistics and use gamified nudges to give positive feedback on healthy food choice. This study protocol describes the design of new pilot studies aimed at measuring the feasibility (acceptability, adherence, and usability) of FRANI and its effects on the quality of food choice of adolescents in Ghana and Vietnam. In each country, 36 adolescents (12-18 years) will be randomly allocated into two groups: The intervention group with the full version of FRANI and the control group with the functionality limited to image recognition and dietary assessment. Participants in both groups will have their food choices tracked for four weeks. The control groups will then switch to the full version of FRANI and both groups will be tracked for a further 2 weeks to assess acceptability, adherence, and usability. Analysis of outcomes will be by intent to treat and differences in outcomes between intervention and control group will use Poisson and odds ratio regression models, accounting for repeated measures at individual levels. If deemed feasible, acceptable and usable, FRANI will address gaps in the literature and advance the nutrition field by potentially improving the quality of food choices of adolescent girls in developing countries. This pilot study will also provide insights on the design of a large randomized controlled trial. The functioning and dissemination of FRANI can be an important step towards highly scalable nutrition data collection and healthier food choices for a population at risk of malnutrition. The study protocol and the methods and materials were approved by the Institutional Review Board (IRB) of the IFPRI on April 29th, 2020 (registration number #00007490), the Thai Nguyen National Hospital on April 14th, 2020 (protocol code 274/ĐĐĐ-BVTWTN) and the University of Ghana on August 10th, 2020 (Federalwide Assurance FWA 00001824; NMIMR-IRB CPN 078-19/20). The study protocol was registered in the International Standard Randomized Controlled Trial Number (ISRCTN 10681553; https://doi.org/10.1186/ISRCTN10681553) on November 12, 2021.

Exploring an Artificial Intelligence–Based, Gamified Phone App Prototype to Track and Improve Food Choices of Adolescent Girls in Vietnam: Acceptability, Usability, and Likeability Study

Background

Adolescents’ consumption of healthy foods is suboptimal in low- and middle-income countries. Adolescents’ fondness for games and social media and the increasing access to smartphones make apps suitable for collecting dietary data and influencing their food choices. Little is known about how adolescents use phones to track and shape their food choices.

Objective

This study aimed to examine the acceptability, usability, and likability of a mobile phone app prototype developed to collect dietary data using artificial intelligence–based image recognition of foods, provide feedback, and motivate users to make healthier food choices. The findings were used to improve the design of the app.

Methods

A total of 4 focus group discussions (n=32 girls, aged 15-17 years) were conducted in Vietnam. Qualitative data were collected and analyzed by grouping ideas into common themes based on content analysis and ground theory.

Results

Adolescents accepted most of the individual- and team-based dietary goals presented in the app prototype to help them make healthier food choices. They deemed the overall app wireframes, interface, and graphic design as acceptable, likable, and usable but suggested the following modifications: tailored feedback based on users’ medical history, anthropometric characteristics, and fitness goals; new language on dietary goals; provision of information about each of the food group dietary goals; wider camera frame to fit the whole family food tray, as meals are shared in Vietnam; possibility of digitally separating food consumption on shared meals; and more appealing graphic design, including unique badge designs for each food group. Participants also liked the app’s feedback on food choices in the form of badges, notifications, and statistics. A new version of the app was designed incorporating adolescent’s feedback to improve its acceptability, usability, and likability.

Conclusions

A phone app prototype designed to track food choice and help adolescent girls from low- and middle-income countries make healthier food choices was found to be acceptable, likable, and usable. Further research is needed to examine the feasibility of using this technology at scale.

Using scenario‐based assessments to examine the feasibility of integrating preventive nutrition services through the primary health care system in Bangladesh

The National Nutrition Services of Bangladesh aims to deliver nutrition services through the primary health care system. Little is known about the feasibility of reshaping service delivery to close gaps in nutrition intervention coverage and utilization. We used a scenario‐based feasibility testing approach to assess potential implementation improvements to strengthen service delivery. We conducted in‐depth interviews with 31 service providers and 12 policymakers, and 5 focus group discussions with potential beneficiaries. We asked about the feasibility of four hypothetical scenarios for preventive and promotive nutrition service delivery: community‐based events (CBE) for pregnant women, well‐child services integrated into immunization contacts; CBE for well‐children, and well‐child visits at facilities. Opinions on service delivery platforms were mixed; some recommended new platforms, but others suggested strengthening existing delivery points. CBE for pregnant women was perceived as feasible, but workforce shortages emerged as a key barrier. Challenges such as equipment portability, upset children and a fast‐moving service environment suggested low feasibility of integrating nutrition into outreach immunization contacts. In contrast, CBE and facility‐based well‐child visits emerged as feasible options, conditional on having the necessary workforce, structural readiness and budget support. On the demand side, enabling factors include using interpersonal communication and involving community leaders to increase awareness, organizing events at a convenient time and place for both providers and beneficiaries, and incentives for beneficiaries to encourage participation. In conclusion, integrating preventive and promotive nutrition services require addressing current challenges in the health system, including human resource and logistic gaps, and investing in creating demand for preventive services.

This study uses a scenario‐based feasibility testing approach to explore potential interventions to strengthen preventive and promotive nutrition service delivery through the primary health care system.

Our findings highlight three highly feasible potential platforms (community‐based events [CBE] for pregnant women, CBE for well‐children and well‐child visits at facilities) to expand preventive services. Scaling these community‐based services requires addressing current challenges in the health system (including human resource and logistic gaps) and investment in demand creation for these services.

SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation

The emergence of the variant of concern Omicron (B.1.1.529) of the severe acute respiratory syndrome coronavirus 2 has aggravated the Covid-19 pandemic due to its very contagious ability. The high infection rate may be due to the high binding affinity of Omicron to human cells, but both experimental and computational studies have yielded conflicting results on this issue. Some studies have shown that the Omicron variant binds to human angiotensin-converting enzyme 2 (hACE2) more strongly than the wild type (WT), but other studies have reported comparable binding affinities. To shed light on this open problem, in this work, we calculated the binding free energy of the receptor binding domain (RBD) of the WT and Omicron spike protein to hACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. We showed that Omicron binds to human cells more strongly than the WT due to increased RBD charge, which enhances electrostatic interaction with negatively charged hACE2. N440K, T478K, E484A, Q493R, and Q498R mutations in the RBD have been found to play a critical role in the stability of the RBD-hACE2 complex. The effect of homogeneous and heterogeneous models of glycans coating the viral RBD and the peptidyl domain of hACE2 was examined. Although the total binding free energy is not sensitive to the glycan model, the distribution of per-residue interaction energies depends on it. In addition, glycans have a little effect on the binding affinity of the WT RBD to hACE2.

Molecular Dynamics Simulations of the Tau Amyloid Fibril Core Dimer at the Surface of a Lipid Bilayer Model: I. In Alzheimer's Disease

A tau R3-R4 domain spanning residues 306-378 was shown to form an amyloid fibril core of a full-length tau in the brain of patients with Alzheimer's disease. Recently, we studied the dynamics of a tau R3-R4 monomer at the surface of a lipid bilayer model and revealed deep insertion of the amino acids spanning the PHF6 motif (residues 306-311) and its flanking residues. Here, we explore the membrane-associated conformational ensemble of a tau R3-R4 dimer by means of atomistic molecular dynamics. Similar to the monomer simulation, the R3-R4 dimer has the propensity to form β-hairpin-like conformation. Unlike the monomer, the dimer shows insertion of the C-terminal R4 region and transient adsorption of the PHF6 motif. Taken together, these results reveal the multiplicity of adsorption and insertion modes of tau into membranes depending on its oligomer size.

Molecular Dynamics Simulations of the Tau R3-R4 Domain Monomer in the Bulk Solution and at the Surface of a Lipid Bilayer Model

The aggregation of the tau protein plays a significant role in Alzheimer's disease, and the tau R3-R4 domain spanning residues 306-378 was shown to form the amyloid fibril core of a full-length tau. The conformations of the tau R3-R4 monomer in the bulk solution and at the surface of membranes are unknown. In this study, we address these questions by means of atomistic molecular dynamics. The simulations in the bulk solution show a very heterogeneous ensemble of conformations with low β and helical contents. The tau R3-R4 monomer has the propensity to form transient β-hairpins within the R3 repeat and between the R3 and R4 repeats and parallel β-sheets spanning the R3 and R4 repeats. The simulations also show that the surface of the membrane does not induce β-sheet insertion and leads to an ensemble of structures very different from those in the bulk solution. They also reveal the dynamical properties of the membrane-bound state of the tau R3-R4 monomer, enabling insertion of the residues 306-318 and 376-378.

Gaps in the implementation and uptake of maternal nutrition interventions in antenatal care services in Bangladesh, Burkina Faso, Ethiopia and India

Antenatal care (ANC) is the largest health platform globally for delivering maternal nutrition interventions (MNIs) to pregnant women. Yet, large missed opportunities remain in nutrition service delivery. This paper examines how well evidence‐based MNIs were incorporated in national policies and programs in Bangladesh, Burkina Faso, Ethiopia and India. We compared the nutrition content of ANC protocols against global recommendations. We used survey data to elucidate the coverage of micronutrient supplementation, weight gain monitoring, dietary and breastfeeding counselling. We reviewed literature, formative research and program assessments to identify barriers and enabling factors of service provision and maternal nutrition practices. Nutrition information in national policies and protocols was often fragmented, incomplete and did not consistently follow global recommendations. Nationally representative data on MNIs in ANC was inadequate, except for iron and folic acid supplementation. Coverage data from subnational surveys showed similar patterns of strengths and weaknesses. MNI coverage was consistently lower than ANC coverage with the lowest coverage of weight gain monitoring and variable coverage of dietary and breastfeeding counselling. Key common factors associated with coverage were micronutrient supply disruptions; suboptimal counselling on maternal diet, weight gain, and breastfeeding; and limited or no record keeping. Adherence of women to micronutrient supplementation and dietary recommendations was low and associated with late and too few ANC contacts, poor maternal knowledge and self‐efficacy, and insufficient family and community support. Models of comprehensive nutrition protocols and health systems that deliver maternal nutrition services in ANC are urgently needed along with national data systems to track progress.

Delivering nutrition services to all pregnant women is essential for maternal and child health outcomes but remains a challenge.

Nutrition gaps in antenatal care (ANC) include lack of specificity in national guidelines and protocols, bottlenecks in micronutrient supplies, low ANC provider knowledge and skills, inadequate supervision to reinforce counseling, and not engaging families to encourage key practices.

National protocols for ANC should be more specific for the four nutrition interventions (micronutrient supplements, weight gain monitoring, counseling on diets and counseling on breastfeeding) and assign accountability for coverage and quality.

Country models are needed for improving provision and utilisation of nutrition interventions through ANC that are based on comprehensive policy frameworks.

Small Oligomers of Aβ42 Protein in the Bulk Solution with AlphaFold2

Aggregation of amyloid-β (Aβ42) protein is one hallmark of Alzheimer's disease, and the conformations of the smallest Aβ42 oligomers are largely unknown. Here, we explore the application of the deep learning AlphaFold2 method to the structure determination of Aβ42 monomers up to hexamers. The results shed light on the early Aβ42 aggregation steps in the bulk solution.

Elastic moduli of normal and cancer cell membranes revealed by molecular dynamics simulations

Recent studies indicate that there are mechanical differences between normal cells and cancer cells. Because the cell membrane takes part in a variety of vital processes, we test the hypothesis of whether or not two fundamental alterations in the cell membrane, i.e., the overexpression of phosphatidylserine lipids in the outer leaflet and a reduction in cholesterol concentration, could cause the softening in cancer cells. Adopting ten models of normal and cancer cell membranes, we carry out 1 μs all-atom molecular dynamics simulations to compare the structural properties and elasticity properties of two membrane types. We find that the overexpression of the phosphatidylserine lipids in the outer leaflet does not significantly alter the area per lipid, the membrane thickness, the lipid order parameters and the elasticity moduli of the cancer membranes. However, a reduction in the cholesterol concentration leads to clear changes in those quantities, especially decreases in the bending, tilt and twist moduli. This implies that the reduction of cholesterol concentration in the cancer membranes could contribute to the softening of cancer cells.

Effect of Cholesterol Molecules on Aβ1-42 Wild-Type and Mutants Trimers

Alzheimer’s disease displays aggregates of the amyloid-beta (Aβ) peptide in the brain, and there is increasing evidence that cholesterol may contribute to the pathogenesis of the disease. Though many experimental and theoretical studies have focused on the interactions of Aβ oligomers with membrane models containing cholesterol, an understanding of the effect of free cholesterol on small Aβ42 oligomers is not fully established. To address this question, we report on replica exchange with a solute tempering simulation of an Aβ42 trimer with cholesterol and compare it with a previous replica exchange molecular dynamics simulation. We show that the binding hot spots of cholesterol are rather complex, involving hydrophobic residues L17–F20 and L30–M35 with a non-negligible contribution of loop residues D22–K28 and N-terminus residues. We also examine the effects of cholesterol on the trimers of the disease-causing A21G and disease-protective A2T mutations by molecular dynamics simulations. We show that these two mutations moderately impact cholesterol-binding modes. In our REST2 simulations, we find that cholesterol is rarely inserted into aggregates but rather attached as dimers and trimers at the surface of Aβ42 oligomers. We propose that cholesterol acts as a glue to speed up the formation of larger aggregates; this provides a mechanistic link between cholesterol and Alzheimer’s disease.

Changes in anemia and anthropometry during adolescence predict learning outcomes: findings from a 3-year longitudinal study in India

BACKGROUND

Anemia and poor physical growth during adolescence have far-ranging consequences, but limited longitudinal evidence exists on how changes in these factors relate to changes in learning skills as adolescents mature.

OBJECTIVES

We examined the association between changes in anemia and physical growth during adolescence and learning outcomes.

METHODS

We used longitudinal data from the Understanding the Lives of Adolescents and Young Adults (UDAYA) project, which surveyed adolescents aged 10-19 y in northern India in 2015-2016 and 2018-2019 (n = 5963). We used multilevel mixed-effects logistic regression models to examine associations between changes in anemia/thinness/stunting status (4 groups: never, improved, new, and persistent) and reading (ability to read a story) and math proficiency (ability to solve division problems) at follow-up.

RESULTS

Persistent anemia and stunting were higher among girls than among boys (46% compared with 8% and 37% compared with 14%, respectively), but persistent thinness was lower (7% compared with 16%). Improvement in anemia, thinness, and stunting was 1.4-1.7 times higher among boys than among girls. Boys who were anemic in both waves were 74% [adjusted odds ratio (AOR): 0.26; 95% CI: 0.12, 0.59] and 65% (AOR: 0.35; 95% CI: 0.16, 0.76) less likely to be able to read a story and solve division problems, respectively, than boys who were nonanemic in both waves. Persistent thinness in boys was negatively associated with both reading (AOR: 0.37; 95% CI: 0.21, 0.66) and math proficiency (AOR: 0.27; 95% CI: 0.16, 0.46). Persistent stunting contributed to lower reading and math proficiency in boys and girls (AORs: 0.29-0.46). Boys whose anemia or thinness status improved and girls whose stunting status improved had similar learning skills at follow-up as those who were never anemic/thin/stunted.

CONCLUSIONS

Persistent anemia, thinness, and short stature during adolescence were associated with poor learning. Programs targeted at adolescents should contribute to nurturing environments that foster healthy growth and learning.

Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation

Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.

Specificity Matters: Unpacking Impact Pathways of Individual Interventions within Bundled Packages Helps Interpret the Limited Impacts of a Maternal Nutrition Intervention in India

BACKGROUND

To address gaps in coverage and quality of nutrition services, Alive & Thrive (A&T) strengthened the delivery of maternal nutrition interventions through government antenatal care (ANC) services in Uttar Pradesh, India. The impact evaluation of the A&T interventions compared intensive ANC (I-ANC) with standard ANC (S-ANC) areas and found modest impacts on micronutrient supplementation, dietary diversity, and weight-gain monitoring.

OBJECTIVES

This study examined intervention-specific program impact pathways (PIPs) and identified reasons for limited impacts of the A&T maternal nutrition intervention package.

METHODS

We used mixed methods: frontline worker (FLW) surveys (n = ∼500), counseling observations (n = 407), and qualitative in-depth interviews with FLWs, supervisors, and block-level staff (n = 59). We assessed 7 PIP domains: training and materials, knowledge, supportive supervision, supply chains, data use, service delivery, and counseling.

RESULTS

Exposure to training improved in both I-ANC and S-ANC areas with more job aids used in I-ANC compared with S-ANC (90% compared with 70%), but gaps remained for training content and refresher trainings. FLWs' knowledge improvement was higher in I-ANC than S-ANC (22-36 percentage points), but knowledge of micronutrient supplement benefits and recommended foods was insufficient (<50%). Most FLWs received supervision (>90%), but supportive supervision was limited by staff vacancies and competing work priorities. Supplies of iron-folic acid and calcium supplements were low in both areas (30-50% stock-outs). Use of monitoring data during review meetings was higher in I-ANC than S-ANC (52% compared with 36%) but was constrained by time, understanding, and data quality. Service provision improved in both I-ANC and S-ANC areas, but counseling on supplement benefits and weight-gain monitoring was low (30-40%).

CONCLUSIONS

Systems-strengthening efforts improved maternal nutrition interventions in ANC, but gaps remained. Taking an intervention-specific perspective to the PIP analysis in this package of services was critical to understand how common and specific barriers influenced overall program impact.

Findings from a tandem clinician leadership intervention for emergency department cardiac arrest care during the COVID-19 pandemic

Introduction

Cardiopulmonary arrest (CPA) care in the Emergency Department (ED) has had to be modified during the coronavirus disease (COVID-19) pandemic. Scarce literature exists on comfort of clinicians (defined as physicians, nurses & advanced practice providers-APP's) in these new roles and their perceived understanding of new algorithms.

Methods

Routine CPA care in our ED was modified during the COVID-19 pandemic. This involved clinicians in shared leadership roles alongside COVID-19 specific changes to CPA algorithms. The new protocol was operationalized through a two-step educational intervention involving didactic education and in-situ simulations. Univariate analyses using student's t-test assessed effectiveness of this educational intervention with clinician comfort as team leaders and perceived knowledge as primary outcomes on a scale of 1 (strongly disagree) to 5 (strongly agree). Subgroup analysis across physicians (attending & resident), nurses & APP's were also undertaken with an alpha of 0.05, and p values <0.05 were considered statistically significant. Secondary outcomes of task saturation, procedural safety and error prevention were also analyzed.

Results

Across 83 of 95 total participants, our primary outcome of clinician comfort in the team leader role improved from a mean value of 3.41 (SD: 1.23) pre-intervention to 4.11 (SD: 0.88) with a p-value <0.001 post intervention. Similar and statistically significant findings in clinician comfort were noted across all subgroups except attending physicians and APP's. Perceived knowledge increased from a mean value of 3.54 (SD: 1.06) pre-intervention to a mean value of 4.24 (SD: 0.67) with a p-value <0.001 post intervention. Similar and statistically significant findings in perceived knowledge were noted across all subgroups except APP's. Responses were registered in either the strongly agree or agree category with regards to task saturation (89%), procedural safety (93%) and error prevention (71%) across all clinicians post intervention.

Conclusion

Our pilot investigation of the effectiveness of an educational intervention of a novel CPA protocol in the ED during the COVID-19 pandemic reached statistical significance with regards to clinician comfort in shared leadership roles and perceived knowledge. These findings suggest that the protocol is rapidly teachable, usable and can be efficiently disseminated across ED clinicians of varying experience, especially in pandemic settings. Further work regarding effectiveness of this new protocol in real life cardiac arrest scenarios is warranted.

COVID-19 Disrupted Provision and Utilization of Health and Nutrition Services in Uttar Pradesh, India: Insights from Service Providers, Household Phone Surveys, and Administrative Data

BACKGROUND

The coronavirus (COVID-19) pandemic may substantially affect health systems, but little primary evidence is available on disruption of health and nutrition services.

OBJECTIVES

This study aimed to 1) determine the extent of disruption in provision and utilization of health and nutrition services induced by the pandemic in Uttar Pradesh, India; and 2) identify how adaptations were made to restore service provision in response to the pandemic.

METHODS

We conducted longitudinal surveys with frontline workers (FLWs, n = 313) and mothers of children <2 y old (n = 659) in December 2019 (in-person) and July 2020 (by phone). We also interviewed block-level managers and obtained administrative data. We examined changes in service provision and utilization using Wilcoxon matched-pairs signed-rank tests.

RESULTS

Compared with prepandemic, service provision reduced substantially during lockdown (83-98 percentage points, pp), except for home visits and take-home rations (∼30%). Most FLWs (68%-90%) restored service provision in July 2020, except for immunization and hot cooked meals (<10%). Administrative data showed similar patterns of disruption and restoration. FLW fears, increased workload, inadequate personal protective equipment (PPE), and manpower shortages challenged service provision. Key adaptations made to provide services were delivering services to beneficiary homes (∼40%-90%), social distancing (80%), and using PPE (40%-50%) and telephones for communication (∼20%). On the demand side, service utilization reduced substantially (40-80 pp) during the lockdown, but about half of mothers received home visits and food supplementation. Utilization for most services did not improve after the lockdown, bearing the challenges of limited travel (30%), nonavailability of services (26%), and fear of catching the virus when leaving the house (22%) or meeting service providers (14%).

CONCLUSIONS

COVID-19 disrupted the provision and use of health and nutrition services in Uttar Pradesh, India, despite adaptations to restore services. Strengthening logistical support, capacity enhancement, performance management, and demand creation are needed to improve service provision and utilization during and post-COVID-19.

Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study

The use of ultrasound in combination with liposomes is a promising approach to improve drug delivery. To achieve an optimal drug release rate, it is important to understand how ultrasound induces pathways on the liposome surface where drugs can be released from the liposome. To this end, we carry out large-scale ultrasound-induced molecular dynamics simulations for three single lipid component liposomes formed from the commonly used phospholipids: 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoylphosphatidylcholine (DPPC), or phosphatidylcholine (POPC). The results show that ultrasound induces the detachment of two leaflets of the DOPC surface, suggesting that the drug release pathway may be through the low lipid packing areas on the stretched surface. In contrast, ultrasound induces pore formation on the surface of DPPC and DOPC, where drugs could escape from the liposomes. While the leaflet detachment and transient pore formation are the mechanisms of DOPC and DPPC, respectively, in both liquid-ordered and liquid-disordered phases, the leaflet detachment mechanism is switched to the transient pore formation mechanism on going from the liquid-ordered phase to the liquid-disordered phase in the POPC liposome. By adding 30% mol cholesterol, the leaflet detachment mechanism is observed in all liposomes. We found that the molecular origin that determines a mechanism is the competition between the intraleaflet and interleaflet interacting energy of lipids. The connection to experimental and theoretical modeling is discussed in some detail.

The role of the state government, civil society and programmes across sectors in stunting reduction in Chhattisgarh, India, 2006-2016

Introduction

Childhood stunting has declined in India between 2006 and 2016, but not uniformly across all states. Little is known about what helped some states accelerate progress while others did not. Insights on subnational drivers of progress are useful not just for India but for other decentralised policy contexts. Thus, we aimed to identify the factors that contributed to declines in childhood stunting (from 52.9% to 37.6%) between 2006 and 2016 in the state of Chhattisgarh, a subnational success story in stunting reduction in India.

Methods

We examined time trends in determinants of stunting using descriptive and regression decomposition analysis of National Family Health Survey data from 2005 to 2006 and 2015–2016. We reviewed nutrition-relevant policies and programmes associated with the drivers of change to construct a policy timeline. Finally, we interviewed multiple stakeholders in the state to understand the changes in the drivers of undernutrition.

Results

The regression decomposition analysis shows that multiple factors explain 66% of the change in stunting between 2006 and 2016. Improvements in three key drivers—health and nutrition services, household assets, and sanitation and hygiene—explained 47% of the change in stunting. A shared vision for impact, political stability and capable bureaucracy, state-level innovations, support from development partners and civil society, and community mobilisation were found to contribute to improvements in programmes for health, poverty and sanitation.

Conclusion

Change in multiple sectors is important for stunting reduction and can be achieved in subnational contexts. More work lies ahead to close gaps in various determinants of stunting.

Understanding Implementation and Improving Nutrition Interventions: Barriers and Facilitators of Using Data Strategically to Inform the Implementation of Maternal Nutrition in Uttar Pradesh, India

BACKGROUND

In response to the high levels of maternal nutrition in Uttar Pradesh, Alive & Thrive (A&T) aimed to strengthen the delivery of nutrition interventions through the government antenatal care platform, including leveraging ongoing data collection to improve program delivery and reach (registered at clinicaltrials.gov as NCT03378141). However, we have a limited understanding of providers' experiences and challenges in collecting and using data for decision making.

OBJECTIVE

The aim was to identify barriers and facilitators to the 1) collection of data and 2) use of data for decision making.

METHODS

In-depth interviews (n = 35) were conducted among block-level government staff, frontline worker (FLW) supervisors, and A&T staff in 2 districts in Uttar Pradesh. Systematic coding of verbatim transcripts and detailed summaries were undertaken to elucidate themes related to data collection and use. FLW supervisors (n = 103) were surveyed to assess data use experiences.

RESULTS

Data were used to understand the reach of maternal nutrition services, estimate the demand for supplements, and guide identification of areas of low FLW performance. About half of supervisors reported using data to identify areas of improvement; however, only 23% reported using data to inform decision making. Facilitators of data collection and use included collaboration between health department officials, perceived importance of block ranking, and monthly review meetings with staff and supervisors to review and discuss data. Barriers to data collection and use included human resource gaps, inadequate technology infrastructure, FLW educational level, political structure, and lack of cooperation between FLWs and supervisors.

CONCLUSIONS

The use of data for decision making is critical for supporting intervention planning and providing targeted supervision and support for FLWs. Despite intensive data-collection efforts, the use of data to inform decision making remains limited. Collaboration facilitated data collection and use, but structural barriers such as staff vacancies need to be addressed to improve the implementation of maternal nutrition interventions.

Strengthening Nutrition Interventions in Antenatal Care Services Affects Dietary Intake, Micronutrient Intake, Gestational Weight Gain, and Breastfeeding in Uttar Pradesh, India: Results of a Cluster-Randomized Program Evaluation

BACKGROUND

Maternal nutrition interventions are inadequately integrated into antenatal care (ANC). Alive & Thrive aimed to strengthen delivery of micronutrient supplements and intensify interpersonal counseling and community mobilization through government ANC services.

OBJECTIVES

We compared nutrition-intensified ANC (I-ANC) with standard ANC (S-ANC) on coverage of nutrition interventions and maternal nutrition practices.

METHODS

We used a cluster-randomized design with cross-sectional baseline (2017) and endline (2019) surveys (n ∼660 pregnant and 1800 recently delivered women per survey) and a repeated-measures longitudinal study in 2018-2019 (n = 400). We derived difference-in-difference effect estimates (DIDs) for diet diversity, consumption of micronutrient supplements, weight monitoring, and early breastfeeding practices.

RESULTS

Despite substantial secular improvements in service coverage from India's national nutrition program, women in the I-ANC arm received more home visits [DID: 7-14 percentage points (pp)] and counseling on core nutrition messages (DID: 10-23 pp) than in the S-ANC arm. One-third of women got ≥3 home visits and one-fourth received ≥4 ANC check-ups in the I-ANC arm. Improvements were greater in the I-ANC arm than in the S-ANC arm for any receipt and consumption of iron-folic acid (DID: 7.5 pp and 9.5 pp, respectively) and calcium supplements (DID: 14.1 pp and 11.5 pp, respectively). Exclusive breastfeeding improved (DID: 7.5 pp) but early initiation of breastfeeding did not. Maternal food group consumption (∼4 food groups) and probability of adequacy of micronutrients (∼20%) remained low in both arms. Repeated-measures longitudinal analyses showed similar results, with additional impact on consumption of vitamin A-rich foods (10 pp, 11 g/d), other vegetables and fruits (22-29 g/d), and gestational weight gain (0.4 kg).

CONCLUSIONS

Intensifying nutrition in government ANC services improved maternal nutrition practices even with strong secular trends in service coverage. Dietary diversity, supplement consumption, and breastfeeding practices remained suboptimal. Achieving greater behavior changes will require strengthening the delivery and use of maternal nutrition services integrated into ANC services in the health system. This trial was registered at clinicaltrials.gov as NCT03378141.

Preconception micronutrient supplementation positively affects child intellectual functioning at 6 y of age: A randomized controlled trial in Vietnam

BACKGROUND

Although there is growing evidence on the role of preconception nutrition for birth outcomes, very few studies have evaluated the long-term effects of nutrition interventions during the preconception period on offspring cognitive outcomes.

OBJECTIVE

We evaluate the impact of preconception weekly multiple micronutrients (MMs) or iron and folic acid (IFA) supplementation compared with folic acid (FA) alone on offspring intellectual functioning at age 6-7 y.

METHODS

We followed 1599 offspring born to women who participated in a double-blinded randomized controlled trial of preconception supplementation in Vietnam. Women received weekly supplements containing either 2800 μg FA only, 60 mg iron and 2800 μg FA, or MMs (15 micronutrients including IFA) from baseline until conception, followed by daily prenatal IFA supplements until delivery. We used the Wechsler Intelligence Scale for Children to measure full-scale IQ (FSIQ) and 4 related domains of intellectual functioning [Verbal Comprehension Index (VCI), Perceptual Reasoning Index (PRI), Working Memory Index (WMI), and Processing Speed Index (PSI) scores] at 6-7 y. Group comparisons were done using ANOVA tests for all children and the subgroup born to women who consumed the supplements ≥26 wk before conception (per-protocol analyses).

RESULTS

The final sample with data at 6-7 y (n = 1321) was similar for baseline maternal and offspring birth characteristics and age at follow-up by treatment group. Compared with the offspring in the FA group, those in the MM group had higher FSIQ (β = 1.7; 95% CI: 0.1, 3.3), WMI (β = 1.7; 95% CI: 0.2, 3.2), and PSI (β = 2.5; 95% CI: 0.9, 4.1). Similar findings were observed in the per-protocol analyses. There were no significant differences by treatment group for VCI and PRI.

CONCLUSIONS

Preconception supplementation with MMs improved certain domains of intellectual functioning at age 6-7 y compared with FA. These findings suggest the potential for preconception micronutrient interventions to have long-term benefits for offspring cognition.

Impact of the Rat R5G, Y10F, and H13R Mutations on Tetrameric Aβ42 β-Barrel in a Lipid Bilayer Membrane Model

Three amino acid substitutions distinguish rat and human Aβ42 peptides and contribute to the difference in toxicity properties. Indeed, aged rodents rarely develop the characteristic lesions of Alzheimer's disease in contrast to humans. Both peptides form, however, amyloid fibrils in buffer solution, but their affinities to the membrane vary. In particular, there is experimental evidence that the rat Aβ42 peptide does not induce Ca²⁺ fluxes in cells. We recently designed a tetrameric β-barrel structure and showed that this model is severely destabilized for Aβ40 human compared to its Aβ42 human counterpart, explaining the absence of ionic currents of Aβ40 in planar lipid bilayers. In this study, we asked whether our model is destabilized for the rat Aβ42 peptide by using extensive replica exchange molecular dynamics simulation in a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer membrane. Our results show that the much lower propensity of aged rodents to develop Alzheimer's disease symptoms might be correlated to its tetrameric β-barrel stability in the cell membrane.

Molecular mechanism of ultrasound interaction with a blood brain barrier model

The brain is strictly protected by the blood brain barrier preventing the crossing of therapeutics to treat brain diseases. The high and low intensity focused ultrasound methods have been used to temporarily open the blood brain barrier, facilitating the transport of drugs. The methods are very promising because the opening is transient, localized, and noninvasive. However, the molecular mechanism of the opening is unknown, and this limits the development and application of these methods. With this in mind, we carry out a molecular dynamics simulation study to understand the interaction of ultrasound with the cell membrane and the tight junction. Our minimal blood brain barrier model is composed of two lipid bilayers, mimicking two portions of neighboring cells, connected together by a tight junction formed by a pair of two cis-dimers of the claudin-5 protein. Using an experimental ultrasound frequency of 50 MHz, simulations show that at low intensities, ultrasound does not impact the structure of the cell membranes and tight junction, implying that the direct interaction of ultrasound with the blood brain barrier is not responsible for the experimentally observed opening. At high intensities, the ultrasound pulls the monolayers of individual cell membrane lipid bilayers apart, creating air compartments inside the bilayers. This reduces the free energy barrier for the translocation of drugs across the lipid bilayer and enhances drug permeability. At very high intensities, the two monolayers are largely separated, resulting in cell damage and implying that the blood brain barrier is primarily opened at the experimentally observed damaged areas.

Cholesterol Molecules Alter the Energy Landscape of Small Aβ1-42 Oligomers

Small amyloid-β (Aβ) oligomers are believed to be key pathogenic species in Alzheimer's disease (AD). One suggested toxicity mechanism is the detergent model where oligomers remove lipid molecules from the bilayer. Senile plaques of AD patients also accumulate a 1:1 ratio of cholesterol/Aβ. What are the dominant structures of small Aβ42 oligomers with cholesterol molecules in aqueous solution? Here, we answer this question by performing atomistic replica exchange molecular dynamics simulations of Aβ42 dimers and trimers. Our simulations demonstrate that the interactions with cholesterol molecules change completely the energy landscape of small Aβ42 oligomers. This result shows that simulations in the bulk solution cannot recapitulate aggregation in the brain extracellular space.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Nonequilibrium molecular dynamics simulations of infrared laser-induced dissociation of a tetrameric Aβ42 β-barrel in a neuronal membrane model

Experimental studies have reported that the amyloid-β proteins can form pores in cell membranes, and this could be one possible source of toxicity in Alzheimer's disease. Dissociation of these pores could therefore be a potential therapeutic approach. It is known that high photon density free-electron laser experiments and laser-induced nonequilibrium molecular dynamics simulations (NEMD) can dissociate amyloid fibrils at specific frequencies in vitro. Our question is whether NEMD simulations can dissociate amyloid pores in a bilayer mimicking a neuronal membrane, and as an example, we select a tetrameric Aβ42 β-barrel. Our simulations shows that the resonance between the laser field and the amide I vibrational mode of the barrel destabilises all intramolecular and intermolecular hydrogen bonds of Aβ42 and converts the β-barrel to a random/coil disordered oligomer. Starting from this disordered oligomer, extensive standard MD simulations shows sampling of disordered Aβ42 states without any increase of β-sheet and reports that the orientational order of lipids is minimally disturbed. Interestingly, the frequency to be employed to dissociate this beta-barrel is specific to the amino acid sequence. Taken together with our previous simulation results, this study indicates that infrared laser irradiation can dissociate amyloid fibrils and oligomers in bulk solution and in a membrane environment without affecting the surrounding molecules, offering therefore a promising way to retard the progression of AD.

Features of the Energy Spectrum of Cosmic Rays above 2.5×10^{18} eV Using the Pierre Auger Observatory

We report a measurement of the energy spectrum of cosmic rays above 2.5×10^{18}  eV based on 215 030 events. New results are presented: at about 1.3×10^{19}  eV, the spectral index changes from 2.51±0.03(stat)±0.05(syst) to 3.05±0.05(stat)±0.10(syst), evolving to 5.1±0.3(stat)±0.1(syst) beyond 5×10^{19}  eV, while no significant dependence of spectral features on the declination is seen in the accessible range. These features of the spectrum can be reproduced in models with energy-dependent mass composition. The energy density in cosmic rays above 5×10^{18}  eV is [5.66±0.03(stat)±1.40(syst)]×10^{53}  erg Mpc^{-3}.

Nutrient Adequacy Is Low among Both Self-Declared Lacto-Vegetarian and Non-Vegetarian Pregnant Women in Uttar Pradesh

Poor dietary intake during pregnancy remains a significant public health concern, affecting the health of the mother and fetus. This study examines the adequacy of energy, macronutrient, and micronutrient intakes among self-declared lacto-vegetarian and non-vegetarian pregnant women. We analyzed dietary data from 627 pregnant women in Uttar Pradesh, India, using a multiple-pass 24 h diet recall. Compared to non-vegetarians, lacto-vegetarians (~46%) were less likely to report excessive carbohydrate (78% vs. 63%) and inadequate fat intakes (70% vs. 52%). In unadjusted analyses, lacto-vegetarians had a slightly higher mean PA for micronutrients (20% vs. 17%), but these differences were no longer significant after controlling for caste, education, and other demographic characteristics. In both groups, the median intake of 9 out of 11 micronutrients was below the Estimated Average Requirement. In conclusion, the energy and micronutrient intakes were inadequate, and the macronutrient intakes were imbalanced, regardless of stated dietary preferences. Since diets are poor across the board, a range of policies and interventions that address the household food environment, nutrition counseling, behavior change, and supplementation are needed in order to achieve adequate nutrient intake for pregnant women in this population.

Infrared Laser-Induced Amyloid Fibril Dissociation: A Joint Experimental/Theoretical Study on the GNNQQNY Peptide

Neurodegenerative diseases are usually characterized by plaques made of well-ordered aggregates of distinct amyloid proteins. Dissociating these very stable amyloid plaques is a critical clinical issue. In this study, we present a joint mid-infrared free electron laser experiment/nonequilibrium molecular dynamics simulation to understand the dissociation process of a representative example GNNQQNY fibril. By tuning the laser frequency to the amide I band of the fibril, the resonance takes place and dissociation is occurred. With the calculated and observed wide-angle X-ray scattering profiles and secondary structures before and after laser irradiation being identical, we can propose a dissociation mechanism with high confidence from our simulations. We find that dissociation starts in the core of the fibrils by fragmenting the intermolecular hydrogen bonds and separating the peptides and then propagates to the fibril extremities leading to the formation of unstructured expanded oligomers. We suggest that this should be a generic mechanism of the laser-induced dissociation of amyloid fibrils.

Effect of Differences in Month and Location of Measurement in Estimating Prevalence and Trend of Wasting and Stunting in India in 2005-2006 and 2015-2016

BACKGROUND

Child undernutrition in India remains widespread. Data from the National Family Health Survey 3 and 4 (NFHS-3 and NFHS-4) suggest that wasting prevalence has increased while stunting prevalence has declined.

OBJECTIVE

The objectives of this study were to do the following: 1) describe wasting and stunting by month of measurement in India in children <5 y of age in NFHS-3 and NFHS-4 surveys, and 2) test whether differences in the timing of anthropometric data collection and in states between survey years introduced bias in the comparison of estimates of wasting and stunting between NFHS-3 and NFHS-4.

METHODS

Data on wasting and stunting for 42,608 and 232,744 children aged >5 y in the NFHS-3 and NFHS-4 survey rounds were analyzed. Differences in the prevalence of wasting and stunting by month of year and by state of residence were examined descriptively. Regression analyses were conducted to test the sensitivity of the estimate of differences in wasting and stunting prevalence across survey years to both state differences and seasonality.

RESULTS

Examination of the patterns of wasting and stunting by month of measurement and by state across survey years reveal marked variability. When both state and month were adjusted, regardless of the method used to account for sample size, there was a small negative difference from 2005-2006 to 2015-2016 in the prevalence of wasting (-0.8 ± 0.6 percentage points; P = 0.2) and a negative difference in stunting prevalence (-8.3 ± 0.7 percentage points; P < 0.001), indicating a small bias for wasting but not for stunting in unadjusted analyses.

CONCLUSIONS

State and seasonal differences may have introduced bias to the estimated difference in prevalence of wasting between the survey years but did not do so for stunting. Future data collection should be designed to maximize consistency in coverage of both time and place.