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Article ; Online: Using big data for risk stratification of childhood pneumonia in low-income and middle-income countries (LMICs)

Maheen Sheikh / Fyezah Jehan

EBioMedicine, Vol 74, Iss , Pp 103740- (2021)

Challenges and opportunities

2021

Keywords	Medicine ; R ; Medicine (General) ; R5-920
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of potential therapeutic intervening targets by in-silico analysis of nsSNPs in preterm birth-related genes.

Muhammad Bilal Azmi / Waqasuddin Khan / M Kamran Azim / Muhammad Imran Nisar / Fyezah Jehan

PLoS ONE, Vol 18, Iss 3, p e

2023 Volume 0280305

Abstract: Prematurity is the foremost cause of death in children under 5 years of age. Genetics contributes to 25-40% of all preterm births (PTB) yet we still need to identify specific targets for intervention based on genetic pathways. This study involved the ... ...

Abstract	Prematurity is the foremost cause of death in children under 5 years of age. Genetics contributes to 25-40% of all preterm births (PTB) yet we still need to identify specific targets for intervention based on genetic pathways. This study involved the effect of region-specific non-synonymous variations and their transcript level mutational impact on protein functioning and stability by various in-silico tools. This investigation identifies potential therapeutic targets to manage the challenge of PTB, corresponding protein cavities and explores their binding interactions with intervening compounds. We searched 20 genes coding 55 PTB proteins from NCBI. Single Nucleotide Polymorphisms (SNPs) of concerned genes were extracted from ENSEMBL, and filtration of exonic variants (non-synonymous) was performed. Several in-silico downstream protein functional effect prediction tools were used to identify damaging variants. Rare coding variants were selected with an allele frequency of ≤1% in 1KGD, further supported by South Asian ALFA frequencies and GTEx gene/tissue expression database. CNN1, COL24A1, IQGAP2 and SLIT2 were identified with 7 rare pathogenic variants found in 17 transcript sequences. The functional impact analyses of rs532147352 (R>H) of CNN1 computed through PhD-SNP, PROVEAN, SNP&GO, PMut and MutPred2 algorithms showed impending deleterious effects, and the presence of this pathogenic mutation in CNN1 resulted in large decrease in protein structural stability (ΔΔG (kcal/mol). After structural protein identification, homology modelling of CNN1, which has been previously reported as a biomarker for the prediction of PTB, was performed, followed by the stereochemical quality checks of the 3D model. Blind docking approach were used to search the binding cavities and molecular interactions with progesterone, ranked with energetic estimations. Molecular interactions of CNN1 with progesterone were investigated through LigPlot 2D. Further, molecular docking experimentation of CNN1 showed the significant ...
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Nutritional support and prophylaxis of azithromycin for pregnant women to improve birth outcomes in peri-urban slums of Karachi, Pakistan—a protocol of multi-arm assessor-blinded randomized controlled trial (Mumta PW trial)

Ameer Muhammad / Zoha Zahid Fazal / Benazir Baloch / Imran Nisar / Fyezah Jehan / Yasir Shafiq

Trials, Vol 23, Iss 1, Pp 1-

2022 Volume 13

Abstract: Abstract Background Maternal undernutrition is critical in the etiology of poor perinatal outcomes and accounts for 20% of small-for-gestational-age (SGA) births. High levels of food insecurity, antenatal undernourishment, and childhood undernutrition ... ...

Abstract	Abstract Background Maternal undernutrition is critical in the etiology of poor perinatal outcomes and accounts for 20% of small-for-gestational-age (SGA) births. High levels of food insecurity, antenatal undernourishment, and childhood undernutrition necessitate the supplementation of fortified balanced energy protein (BEP) during pregnancy in low-income settings especially with scarce literature available in this subject. Hence, this paper extensively covers the protocol of such a trial conducted in an urban slum of Karachi, Pakistan. Methods The trial is community-based, open-labelled, four-arm, and randomized controlled that will include parallel group assignments with a 1:1:1:1 allocation ratio in low-income squatter settlements in urban Karachi, Pakistan. All pregnant women (PW), if identified between > 8 and < 19 weeks of gestation based on ultrasound, will be offered routine antenatal care (ANC) counseling and voluntary participation in the trial after written informed consent. A total number of 1836 PW will be enrolled with informed consent and randomly allocated to one of the four arms receiving: (1) ANC counseling only (control group), (2) ANC counseling plus BEP supplement (intervention arm 1), (3) ANC counseling plus BEP supplement plus 2 doses azithromycin (intervention arm 2), or (4) ANC counseling plus BEP supplement plus daily single dose of nicotinamide and choline (intervention arm 3). Trial registration ClinicalTrials.gov NCT04012177 . Registered on July 9, 2019.
Keywords	Medicine (General) ; R5-920
Subject code	360
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Intussusception in an infant as a manifestation of COVID-19

Zorays Moazzam / Areej Salim / Alina Ashraf / Fyezah Jehan / Muhammad Arshad

Journal of Pediatric Surgery Case Reports, Vol 59, Iss , Pp 101533- (2020)

2020

Abstract: Gastrointestinal manifestations of COVID-19 are rare and have primarily been limited to diarrhea or vomiting. Intussusception is the most common cause of bowel obstruction in infants, with up to 30% of pediatric intussusception cases having a preceding ... ...

Abstract	Gastrointestinal manifestations of COVID-19 are rare and have primarily been limited to diarrhea or vomiting. Intussusception is the most common cause of bowel obstruction in infants, with up to 30% of pediatric intussusception cases having a preceding viral illness. We present the rare case of intussusception in a SARS-CoV-2 positive infant. This is the first documented case of survival in a SARS-CoV-2 positive patient presenting with intussusception as the primary manifestation. As our knowledge of this disease evolves, surgeons need to remain suspicious for possible gastrointestinal manifestations of COVID-19.
Keywords	COVID-19 ; Intussusception ; Pediatric ; Pediatrics ; RJ1-570 ; Surgery ; RD1-811 ; covid19
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Clinical and epidemiological features of pediatric population hospitalized with COVID-19

Qalab Abbas / Farah Khalid / Fatima Farrukh Shahbaz / Javeria Khan / Shazia Mohsin / Murtaza Ali Gowa / Abdul Sattar Shaikh / Rai Muhammad Asghar / Javairia Khalid / Sehrish Karim / Fyezah Jehan / Masood Sadiq / Junaid Rashid

The Lancet Regional Health - Southeast Asia, Vol 11, Iss , Pp 100176- (2023)

a multicenter longitudinal study (March 2020–December 2021) from PakistanResearch in context

2023

Abstract: Summary: Background: We aimed to explore the epidemiological, clinical, and phenotypic parameters of pediatric patients hospitalized with COVID-19 in Pakistan. Methods: This longitudinal cohort study was conducted in five tertiary care hospitals in ... ...

Abstract	Summary: Background: We aimed to explore the epidemiological, clinical, and phenotypic parameters of pediatric patients hospitalized with COVID-19 in Pakistan. Methods: This longitudinal cohort study was conducted in five tertiary care hospitals in Pakistan from March 2020 to December 2021. Data on various epidemiological and clinical variables were collected using Case Report Forms (CRFs) adapted from the WHO COVID-19 clinical data platform at baseline and at monthly follow-ups for 3 months. Findings: A total of 1090 children were included. The median age was 5 years (Interquartile range 1–10), and the majority presented due to new signs/symptoms associated with COVID-19 (57.8%; n = 631), the most common being general and respiratory symptoms. Comorbidities were present in 417 (38.3%) children. Acute COVID-19 alone was found in 932 (85.5%) children, 81 (7.4%) had multisystem inflammatory syndrome (MIS-C), 77 (7.0%) had overlapping features of acute COVID-19 and MIS-C, and severe disease was found in 775/1086 (71.4%). Steroids were given to 351 (32.2%) patients while 77 (7.1%) children received intravenous immunoglobulins. Intensive care unit (ICU) care was required in 334 (31.6%) patients, and 203 (18.3%) deaths were reported during the study period. The largest spike in cases and mortality was from July to September 2021 when the Delta variant first emerged. During the first and second follow-ups, 37 and 10 children expired respectively, and medical care after discharge was required in 204 (25.4%), 94 (16.6%), and 70 (13.7%) children respectively during each monthly follow-up. Interpretation: Our study highlights that acute COVID-19 was the major phenotype associated with high severity and mortality in children in Pakistan in contrast to what has been observed globally. Funding: The study was supported by the World Health Organization (WHO), which was involved in the study design but played no role in its analysis, writeup, or publication.
Keywords	Pediatric COVID-19 ; Epidemiology ; SARS-CoV-2 ; Pakistan ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Co-carriage of Staphylococcus aureus and Streptococcus pneumoniae among children younger than 2 years of age in a rural population in Pakistan

Shahira Shahid / Muhammad Imran Nisar / Fyezah Jehan / Sheraz Ahmed / Furqan Kabir / Aneeta Hotwani / Sahrish Muneer / Muhammad Farrukh Qazi / Sajid Muhammad / Asad Ali / Anita K.M. Zaidi / Najeeha T. Iqbal

Clinical Epidemiology and Global Health, Vol 21, Iss , Pp 101293- (2023)

2023

Abstract: Objectives: Staphylococcus aureus and Streptococcus pneumoniae are common colonizers of the human nasopharynx. In this study, we describe S. aureus nasopharyngeal carriage and evaluate its association with S. pneumoniae carriage post-10-valent ... ...

Abstract	Objectives: Staphylococcus aureus and Streptococcus pneumoniae are common colonizers of the human nasopharynx. In this study, we describe S. aureus nasopharyngeal carriage and evaluate its association with S. pneumoniae carriage post-10-valent pneumococcal conjugate vaccine (PCV10) introduction in Pakistan. Methods: A serial cross-sectional study was undertaken from 2014 to 2018, children <2 years were randomly selected, and nasopharyngeal swabs were collected using standard WHO guidelines. S. aureus and S. pneumoniae isolates were identified using standard methods and tested for antimicrobial susceptibility by the standard Kirby-Bauer disk-diffusion method as per Clinical & Laboratory Standards Institute (CLSI) recommendations. Regression analysis was used to determine predictors associated with S. aureus carriage. Results: We enrolled 3140 children. S. aureus carriage prevalence was 5.6% (176/3140), and 50.1% (81/176) of the isolates were methicillin-resistant S. aureus (MRSA). S. aureus carriage was higher in the absence of pneumococcus compared to isolates in which pneumococcus was present (7.5% vs 5.0%). S. aureus carriage was negatively associated with pneumococcal carriage, being in 3rd and 4th year of enrollment, and vaccination with two and three PCV10 doses, in addition, fast breathing, ≥2 outpatients visits, and rainy season were positively associated. The following resistance rates were observed: 98.9% for penicillin, 74.4% for fusidic acid, and 23.3% for gentamicin, 10.2% for erythromycin, and 8.5% for cotrimoxazole. All isolates were susceptible to amikacin. Conclusions: Overall S. aureus carriage prevalence was low, PCV10 vaccine was protective against the carriage. The proportion of MRSA carriage and antimicrobial resistance was high in this community warranting continuous monitoring for invasive infections.
Keywords	Nasopharyngeal carriage ; Pakistan ; Streptococcus pneumoniae ; Staphylococcus aureus ; MRSA ; Children ; Public aspects of medicine ; RA1-1270
Subject code	630
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparison of Masimo Total Hemoglobin SpHb® continuous non-invasive hemoglobin monitoring device with laboratory complete blood count measurement using venous sample

Fyezah Jehan / Bellington Vwalika / Emily R. Smith / Fouzia Farooq / Victor Akelo / Sasha Glass Baumann / Zahra Hoodbhoy / Qing Pan / Imran Nisar / Margaret Kasaro / Joan T. Price / Gregory Ouma

Gates Open Research, Vol

Protocol for an observational substudy of the Pregnancy Risk and Infant Surveillance and Measurement Alliance Maternal and Newborn Health (PRISMA MNH) study [version 1; peer review: 2 approved]

2023 Volume 7

Abstract: Background: The Masimo Total Hemoglobin SpHb® is a continuous and non-invasive handheld device to measure hemoglobin levels. Previous research has found that SpHb is able to accurately detect hemoglobin levels in adult patients with a similar degree of ... ...

Abstract	Background: The Masimo Total Hemoglobin SpHb® is a continuous and non-invasive handheld device to measure hemoglobin levels. Previous research has found that SpHb is able to accurately detect hemoglobin levels in adult patients with a similar degree of bias and standard deviation to point-of-care invasive method measurements. Generally, limited clinical evidence, lack of validation of Masimo at higher than and lower than hemoglobin threshold values, and scientific consensus supporting the use of Masimo for accurate hemoglobin testing for the diagnosis of anemia during pregnancy calls for further research. Methods and analysis: The proposed prospective cohort will be nested within the ongoing Pregnancy Risk and Infant Surveillance and Measurement Alliance (PRISMA) Maternal and Newborn Health (MNH) study. Three study sites (located in Zambia, Kenya, and Pakistan) will participate and collect hemoglobin data at five time points (<20 weeks, 20 weeks, 28 weeks, 36 weeks’ gestation, and six weeks postpartum). We will measure hemoglobin using a venous blood sample via hematology auto-analyzer complete blood count (gold standard) and the non-invasive device. The primary objective is to assess agreement between Masimo total hemoglobin and complete blood count and on a continuous scale using Intraclass Correlation Coefficient and Bland-Altman Analysis. The second objective is to assess agreement between the two measures on a binary scale using Positive Percentage Agreement and Negative Percentage Agreement, Cohen’s Kappa, and McNemar Test. On an ordinal scale, agreement will be measured using Weighted Cohen’s Kappa and Harrel’s Concordance Index. Lastly, we will assess factors that might affect the accuracy of Masimo total hemoglobin using linear mixed models. Conclusions: The primary aim of this study is to assess the validity of the non-invasive Masimo device compared to the gold standard method of invasive hemoglobin measurements during pregnancy and postpartum periods for the diagnosis of anemia.
Keywords	hemoglobin ; device validation ; anemia ; pregnancy ; postpartum ; non-invasive ; eng ; Medicine ; R
Subject code	610
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cohort profile

Fyezah Jehan / Uzma Khan / Zahra Hoodbhoy / Emily Smith / Fouzia Farooq / Muhammad Imran Nisar / Ali Jaffar / Sabahat Naz / Nida Yazdani / Muhammad Kashif / Zaid Hussain

BMJ Open, Vol 13, Iss

the Pregnancy Risk Infant Surveillance and Measurement Alliance (PRISMA) – Pakistan

2023 Volume 12

Abstract: Purpose Pakistan has disproportionately high maternal and neonatal morbidity and mortality. There is a lack of detailed, population-representative data to provide evidence for risk factors, morbidities and mortality among pregnant women and their ... ...

Abstract	Purpose Pakistan has disproportionately high maternal and neonatal morbidity and mortality. There is a lack of detailed, population-representative data to provide evidence for risk factors, morbidities and mortality among pregnant women and their newborns. The Pregnancy Risk, Infant Surveillance and Measurement Alliance (PRISMA) is a multicountry open cohort that aims to collect high-dimensional, standardised data across five South Asian and African countries for estimating risk and developing innovative strategies to optimise pregnancy outcomes for mothers and their newborns. This study presents the baseline maternal and neonatal characteristics of the Pakistan site occurring prior to the launch of a multisite, harmonised protocol.Participants PRISMA Pakistan study is being conducted at two periurban field sites in Karachi, Pakistan. These sites have primary healthcare clinics where pregnant women and their newborns are followed during the antenatal, intrapartum and postnatal periods up to 1 year after delivery. All encounters are captured electronically through a custom-built Android application. A total of 3731 pregnant women with a mean age of 26.6±5.8 years at the time of pregnancy with neonatal outcomes between January 2021 and August 2022 serve as a baseline for the PRISMA Pakistan study.Findings to date In this cohort, live births accounted for the majority of pregnancy outcomes (92%, n=3478), followed by miscarriages/abortions (5.5%, n=205) and stillbirths (2.6%, n=98). Twenty-two per cent of women (n=786) delivered at home. One out of every four neonates was low birth weight (<2500 g), and one out of every five was preterm (gestational age <37 weeks). The maternal mortality rate was 172/100 000 pregnancies, the neonatal mortality rate was 52/1000 live births and the stillbirth rate was 27/1000 births. The three most common causes of neonatal deaths obtained through verbal autopsy were perinatal asphyxia (39.6%), preterm births (19.8%) and infections (12.6%).Future plans The PRISMA cohort will ...
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Machine learning from fetal flow waveforms to predict adverse perinatal outcomes

Zahra Hoodbhoy / Babar Hasan / Fyezah Jehan / Bart Bijnens / Devyani Chowdhury

Gates Open Research, Vol

a study protocol [version 1; referees: 2 approved]

2018 Volume 2

Abstract: Background: In Pakistan, stillbirth rates and early neonatal mortality rates are amongst the highest in the world. The aim of this study is to provide proof of concept for using a computational model of fetal haemodynamics, combined with machine learning. ...

Abstract	Background: In Pakistan, stillbirth rates and early neonatal mortality rates are amongst the highest in the world. The aim of this study is to provide proof of concept for using a computational model of fetal haemodynamics, combined with machine learning. This model will be based on Doppler patterns of the fetal cardiovascular, cerebral and placental flows with the goal to identify those fetuses at increased risk of adverse perinatal outcomes such as stillbirth, perinatal mortality and other neonatal morbidities. Methods: This will be prospective one group cohort study which will be conducted in Ibrahim Hyderi, a peri-urban settlement in south east of Karachi. The eligibility criteria include pregnant women between 22-34 weeks who reside in the study area. Once enrolled, in addition to the performing fetal ultrasound to obtain Dopplers, data on socio-demographic, maternal anthropometry, haemoglobin and cardiotocography will be obtained on the pregnant women. Discussion: The machine learning approach for predicting adverse perinatal outcomes obtained from the current study will be validated in a larger population at the next stage. The data will allow for early interventions to improve perinatal outcomes.
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2018-02-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Clinical signs predictive of severe illness in young Pakistani infants

Shahira Shahid / Shiyam Sunder Tikmani / Kanwal Nayani / Ayesha Munir / Nick Brown / Anita K. M. Zaidi / Fyezah Jehan / Muhammad Imran Nisar

BMC Research Notes, Vol 14, Iss 1, Pp 1-

2021 Volume 6

Abstract: Abstract Objective Early detection of specific signs and symptoms to predict severe illness is essential to prevent infant mortality. As a continuation of the results from the multicenter Young Infants Clinical Signs and Symptoms (YICSS) study, we ... ...

Abstract	Abstract Objective Early detection of specific signs and symptoms to predict severe illness is essential to prevent infant mortality. As a continuation of the results from the multicenter Young Infants Clinical Signs and Symptoms (YICSS) study, we present here the performance of the seven-sign algorithm in 3 age categories (0–6 days, 7–27 days and 28–59 days) in Pakistani infants aged 0–59 days. Results From September 2003 to November 2004, 2950 infants were enrolled (age group 0–6 days = 1633, 7–27 days = 817, 28–59 days = 500). The common reason for seeking care was umbilical redness or discharge (29.2%) in the 0–6 days group. Older age groups presented with cough (16.9%) in the 7–27 age group and (26.9%) infants in the 28–59 days group. Severe infection/sepsis was the most common primary diagnoses in infants requiring hospitalization across all age groups. The algorithm performed well in every age group, with a sensitivity of 85.9% and specificity of 71.6% in the 0–6 days age group and a sensitivity of 80.5% and specificity of 80.2% in the 28–59 days group; the sensitivity was slightly lower in the 7–27 age group (72.4%) but the specificity remained high (83.1%).
Keywords	Young infants ; Clinical signs ; Severe illness requiring hospitalization ; Pakistan ; Community ; Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390
Subject code	610
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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