| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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| 4. |
- Day, Louise Tina, et al.
(författare)
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Assessment of the validity of the measurement of newborn and maternal health-care coverage in hospitals (EN-BIRTH): an observational study.
- 2021
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Ingår i: The Lancet. Global health. - : Elsevier. - 2214-109X. ; 9:3, s. e267-e279
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Tidskriftsartikel (refereegranskat)abstract
- Progress in reducing maternal and neonatal deaths and stillbirths is impeded by data gaps, especially regarding coverage and quality of care in hospitals. We aimed to assess the validity of indicators of maternal and newborn health-care coverage around the time of birth in survey data and routine facility register data.Every Newborn-BIRTH Indicators Research Tracking in Hospitals was an observational study in five hospitals in Bangladesh, Nepal, and Tanzania. We included women and their newborn babies who consented on admission to hospital. Exclusion critiera at admission were no fetal heartbeat heard or imminent birth. For coverage of uterotonics to prevent post-partum haemorrhage, early initiation of breastfeeding (within 1 h), neonatal bag-mask ventilation, kangaroo mother care (KMC), and antibiotics for clinically defined neonatal infection (sepsis, pneumonia, or meningitis), we collected time-stamped, direct observation or case note verification data as gold standard. We compared data reported via hospital exit surveys and via hospital registers to the gold standard, pooled using random effects meta-analysis. We calculated population-level validity ratios (measured coverage to observed coverage) plus individual-level validity metrics.We observed 23 471 births and 840 mother-baby KMC pairs, and verified the case notes of 1015 admitted newborn babies regarding antibiotic treatment. Exit-survey-reported coverage for KMC was 99·9% (95% CI 98·3-100) compared with observed coverage of 100% (99·9-100), but exit surveys underestimated coverage for uterotonics (84·7% [79·1-89·5]) vs 99·4% [98·7-99·8] observed), bag-mask ventilation (0·8% [0·4-1·4]) vs 4·4% [1·9-8·1]), and antibiotics for neonatal infection (74·7% [55·3-90·1] vs 96·4% [94·0-98·6] observed). Early breastfeeding coverage was overestimated in exit surveys (53·2% [39·4-66·8) vs 10·9% [3·8-21·0] observed). "Don't know" responses concerning clinical interventions were more common in the exit survey after caesarean birth. Register data underestimated coverage of uterotonics (77·9% [37·8-99·5] vs 99·2% [98·6-99·7] observed), bag-mask ventilation (4·3% [2·1-7·3] vs 5·1% [2·0-9·6] observed), KMC (92·9% [84·2-98·5] vs 100% [99·9-100] observed), and overestimated early breastfeeding (85·9% (58·1-99·6) vs 12·5% [4·6-23·6] observed). Inter-hospital heterogeneity was higher for register-recorded coverage than for exit survey report. Even with the same register design, accuracy varied between hospitals.Coverage indicators for newborn and maternal health care in exit surveys had low accuracy for specific clinical interventions, except for self-report of KMC, which had high sensitivity after admission to a KMC ward or corner and could be considered for further assessment. Hospital register design and completion are less standardised than surveys, resulting in variable data quality, with good validity for the best performing sites. Because approximately 80% of births worldwide take place in facilities, standardising register design and information systems has the potential to sustainably improve the quality of data on care at birth.Children's Investment Fund Foundation and Swedish Research Council.
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| 5. |
- Hossain, Aniqa T., et al.
(författare)
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Measuring coverage and quality of supportive care for inpatient neonatal infections : EN-BIRTH multi-country validation study
- 2022
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Ingår i: Journal of Global Health. - : International Global Health Society. - 2047-2978 .- 2047-2986. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Background: An estimated 7 million episodes of severe newborn infections occur annually worldwide, with half a million newborn deaths, most oc-curring in low-and middle-income countries. Whilst injectable antibiotics are necessary to treat the infection, supportive care is also crucial in ending preventable mortality and morbidity. This study uses multi-country data to assess gaps in coverage, quality, and documentation of supportive care, considering implications for measurement.Methods: The EN-BIRTH study was conducted in five hospitals in Bangla-desh, Nepal, and Tanzania (July 2017-July 2018). Newborns with an ad-mission diagnosis of clinically-defined infection (sepsis, meningitis, and/or pneumonia) were included. Researchers extracted data from inpatient case notes and interviews with women (usually the mothers) as the primary fam-ily caretakers after discharge. The interviews were conducted using a struc-tured survey questionnaire. We used descriptive statistics to report coverage of newborn supportive care components such as oxygen use, photothera-py, and appropriate feeding, and we assessed the validity of measurement through survey-reports using a random-effects model to generate pooled estimates. In this study, key supportive care components were assessment and correction of hypoxaemia, hyperbilirubinemia, and hypoglycaemia.Results: Among 1015 neonates who met the inclusion criteria, 89% had an admission clinical diagnosis of sepsis. Major gaps in documentation and care practices related to supportive care varied substantially across the par-ticipating hospitals. The pooled sensitivity was low for the survey-reported oxygen use (47%; 95% confidence interval (CI) = 30%-64%) and moderate for phototherapy (60%; 95% CI = 44%-75%). The pooled specificity was high for both the survey-reported oxygen use (85%; 95% CI = 80%-89%) and phototherapy (91%; 95% CI = 82%-97%).Conclusions: The women's reports during the exit survey consistently un-derestimated the coverage of supportive care components for managing infection. We have observed high variability in the inpatient documents across facilities. A standardised ward register for inpatient small and sick newborn care may capture selected supportive care data. However, tracking the detailed care will require standardised individual-level data sets linked to newborn case notes. We recommend investments in assessing the im-plementation aspects of a standardised inpatient register in resource-poor settings.
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| 6. |
- Hossain, Aniqa T, et al.
(författare)
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Measuring coverage and quality of supportive care for inpatient neonatal infections: EN-BIRTH multi-country validation study.
- 2022
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Ingår i: Journal of global health. - : International Global Health Society. - 2047-2986 .- 2047-2978. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- An estimated 7 million episodes of severe newborn infections occur annually worldwide, with half a million newborn deaths, most occurring in low- and middle-income countries. Whilst injectable antibiotics are necessary to treat the infection, supportive care is also crucial in ending preventable mortality and morbidity. This study uses multi-country data to assess gaps in coverage, quality, and documentation of supportive care, considering implications for measurement.The EN-BIRTH study was conducted in five hospitals in Bangladesh, Nepal, and Tanzania (July 2017-July 2018). Newborns with an admission diagnosis of clinically-defined infection (sepsis, meningitis, and/or pneumonia) were included. Researchers extracted data from inpatient case notes and interviews with women (usually the mothers) as the primary family caretakers after discharge. The interviews were conducted using a structured survey questionnaire. We used descriptive statistics to report coverage of newborn supportive care components such as oxygen use, phototherapy, and appropriate feeding, and we assessed the validity of measurement through survey-reports using a random-effects model to generate pooled estimates. In this study, key supportive care components were assessment and correction of hypoxaemia, hyperbilirubinemia, and hypoglycaemia.Among 1015 neonates who met the inclusion criteria, 89% had an admission clinical diagnosis of sepsis. Major gaps in documentation and care practices related to supportive care varied substantially across the participating hospitals. The pooled sensitivity was low for the survey-reported oxygen use (47%; 95% confidence interval (CI) = 30%-64%) and moderate for phototherapy (60%; 95% CI = 44%-75%). The pooled specificity was high for both the survey-reported oxygen use (85%; 95% CI = 80%-89%) and phototherapy (91%; 95% CI = 82%-97%).The women's reports during the exit survey consistently underestimated the coverage of supportive care components for managing infection. We have observed high variability in the inpatient documents across facilities. A standardised ward register for inpatient small and sick newborn care may capture selected supportive care data. However, tracking the detailed care will require standardised individual-level data sets linked to newborn case notes. We recommend investments in assessing the implementation aspects of a standardised inpatient register in resource-poor settings.
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| 7. |
- KC, Ashish, 1982, et al.
(författare)
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Neonatal resuscitation: EN-BIRTH multi-country validation study.
- 2021
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Ingår i: BMC pregnancy and childbirth. - : Springer Science and Business Media LLC. - 1471-2393. ; 21:Suppl 1
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Tidskriftsartikel (refereegranskat)abstract
- Annually, 14 million newborns require stimulation to initiate breathing at birth and 6 million require bag-mask-ventilation (BMV). Many countries have invested in facility-based neonatal resuscitation equipment and training. However, there is no consistent tracking for neonatal resuscitation coverage.The EN-BIRTH study, in five hospitals in Bangladesh, Nepal, and Tanzania (2017-2018), collected time-stamped data for care around birth, including neonatal resuscitation. Researchers surveyed women and extracted data from routine labour ward registers. To assess accuracy, we compared gold standard observed coverage to survey-reported and register-recorded coverage, using absolute difference, validity ratios, and individual-level validation metrics (sensitivity, specificity, percent agreement). We analysed two resuscitation numerators (stimulation, BMV) and three denominators (live births and fresh stillbirths, non-crying, non-breathing). We also examined timeliness of BMV. Qualitative data were collected from health workers and data collectors regarding barriers and enablers to routine recording of resuscitation.Among 22,752 observed births, 5330 (23.4%) babies did not cry and 3860 (17.0%) did not breathe in the first minute after birth. 16.2% (n = 3688) of babies were stimulated and 4.4% (n = 998) received BMV. Survey-report underestimated coverage of stimulation and BMV. Four of five labour ward registers captured resuscitation numerators. Stimulation had variable accuracy (sensitivity 7.5-40.8%, specificity 66.8-99.5%), BMV accuracy was higher (sensitivity 12.4-48.4%, specificity > 93%), with small absolute differences between observed and recorded BMV. Accuracy did not vary by denominator option. < 1% of BMV was initiated within 1 min of birth. Enablers to register recording included training and data use while barriers included register design, documentation burden, and time pressure.Population-based surveys are unlikely to be useful for measuring resuscitation coverage given low validity of exit-survey report. Routine labour ward registers have potential to accurately capture BMV as the numerator. Measuring the true denominator for clinical need is complex; newborns may require BMV if breathing ineffectively or experiencing apnoea after initial drying/stimulation or subsequently at any time. Further denominator research is required to evaluate non-crying as a potential alternative in the context of respectful care. Measuring quality gaps, notably timely provision of resuscitation, is crucial for programme improvement and impact, but unlikely to be feasible in routine systems, requiring audits and special studies.
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| 8. |
- Kong, Stefanie, et al.
(författare)
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Birthweight: EN-BIRTH multi-country validation study.
- 2021
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Ingår i: BMC pregnancy and childbirth. - : Springer Science and Business Media LLC. - 1471-2393. ; 21:Suppl 1
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Tidskriftsartikel (refereegranskat)abstract
- Accurate birthweight is critical to inform clinical care at the individual level and tracking progress towards national/global targets at the population level. Low birthweight (LBW) < 2500 g affects over 20.5 million newborns annually. However, data are lacking and may be affected by heaping. This paper evaluates birthweight measurement within the Every Newborn Birth Indicators Research Tracking in Hospitals (EN-BIRTH) study.The EN-BIRTH study took place in five hospitals in Bangladesh, Nepal and Tanzania (2017-2018). Clinical observers collected time-stamped data (gold standard) for weighing at birth. We compared accuracy for two data sources: routine hospital registers and women's report at exit interview survey. We calculated absolute differences and individual-level validation metrics. We analysed birthweight coverage and quality gaps including timing and heaping. Qualitative data explored barriers and enablers for routine register data recording.Among 23,471 observed births, 98.8% were weighed. Exit interview survey-reported weighing coverage was 94.3% (90.2-97.3%), sensitivity 95.0% (91.3-97.8%). Register-reported coverage was 96.6% (93.2-98.9%), sensitivity 97.1% (94.3-99%). Routine registers were complete (> 98% for four hospitals) and legible > 99.9%. Weighing of stillbirths varied by hospital, ranging from 12.5-89.0%. Observed LBW rate was 15.6%; survey-reported rate 14.3% (8.9-20.9%), sensitivity 82.9% (75.1-89.4%), specificity 96.1% (93.5-98.5%); register-recorded rate 14.9%, sensitivity 90.8% (85.9-94.8%), specificity 98.5% (98-99.0%). In surveys, "don't know" responses for birthweight measured were 4.7%, and 2.9% for knowing the actual weight. 95.9% of observed babies were weighed within 1 h of birth, only 14.7% with a digital scale. Weight heaping indices were around two-fold lower using digital scales compared to analogue. Observed heaping was almost 5% higher for births during the night than day. Survey-report further increased observed birthweight heaping, especially for LBW babies. Enablers to register birthweight measurement in qualitative interviews included digital scale availability and adequate staffing.Hospital registers captured birthweight and LBW prevalence more accurately than women's survey report. Even in large hospitals, digital scales were not always available and stillborn babies not always weighed. Birthweight data are being captured in hospitals and investment is required to further improve data quality, researching of data flow in routine systems and use of data at every level.
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| 9. |
- Peven, Kimberly, et al.
(författare)
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Stillbirths including intrapartum timing: EN-BIRTH multi-country validation study.
- 2021
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Ingår i: BMC pregnancy and childbirth. - : Springer Science and Business Media LLC. - 1471-2393. ; 21:Suppl 1
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Tidskriftsartikel (refereegranskat)abstract
- An estimated >2 million babies stillborn around the world each year lack visibility. Low- and middle-income countries carry 84% of the burden yet have the least data. Most births are now in facilities, hence routine register-recording presents an opportunity to improve counting of stillbirths, but research is limited, particularly regarding accuracy. This paper evaluates register-recorded measurement of hospital stillbirths, classification accuracy, and barriers and enablers to routine recording.The EN-BIRTH mixed-methods, observational study took place in five hospitals in Bangladesh, Nepal and Tanzania (2017-2018). Clinical observers collected time-stamped data on perinatal care and birth outcomes as gold standard. To assess accuracy of routine register-recorded stillbirth rates, we compared birth outcomes recorded in labour ward registers to observation data. We calculated absolute rate differences and individual-level validation metrics (sensitivity, specificity, percent agreement). We assessed misclassification of stillbirths with neonatal deaths. To examine stillbirth appearance (fresh/macerated) as a proxy for timing of death, we compared appearance to observed timing of intrauterine death based on heart rate at admission.23,072 births were observed including 550 stillbirths. Register-recorded completeness of birth outcomes was > 90%. The observed study stillbirth rate ranged from 3.8 (95%CI = 2.0,7.0) to 50.3 (95%CI = 43.6,58.0)/1000 total births and was under-estimated in routine registers by 1.1 to 7.3 /1000 total births (register: observed ratio 0.9-0.7). Specificity of register-recorded birth outcomes was > 99% and sensitivity varied between hospitals, ranging from 77.7-86.1%. Percent agreement between observer-assessed birth outcome and register-recorded birth outcome was very high across all hospitals and all modes of birth (> 98%). Fresh or macerated stillbirth appearance was a poor proxy for timing of stillbirth. While there were similar numbers of stillbirths misclassified as neonatal deaths (17/430) and neonatal deaths misclassified as stillbirths (21/36), neonatal deaths were proportionately more likely to be misclassified as stillbirths (58.3% vs 4.0%). Enablers to more accurate register-recording of birth outcome included supervision and data use.Our results show these routine registers accurately recorded stillbirths. Fresh/macerated appearance was a poor proxy for intrapartum stillbirths, hence more focus on measuring fetal heart rate is crucial to classification and importantly reduction in these preventable deaths.
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| 10. |
- Rahman, Ahmed Ehsanur, et al.
(författare)
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Antibiotic use for inpatient newborn care with suspected infection: EN-BIRTH multi-country validation study.
- 2021
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Ingår i: BMC pregnancy and childbirth. - : Springer Science and Business Media LLC. - 1471-2393. ; 21:Suppl 1
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Tidskriftsartikel (refereegranskat)abstract
- An estimated 30 million neonates require inpatient care annually, many with life-threatening infections. Appropriate antibiotic management is crucial, yet there is no routine measurement of coverage. The Every Newborn Birth Indicators Research Tracking in Hospitals (EN-BIRTH) study aimed to validate maternal and newborn indicators to inform measurement of coverage and quality of care. This paper reports validation of reported antibiotic coverage by exit survey of mothers for hospitalized newborns with clinically-defined infections, including sepsis, meningitis, and pneumonia.EN-BIRTH study was conducted in five hospitals in Bangladesh, Nepal, and Tanzania (July 2017-July 2018). Neonates were included based on case definitions to focus on term/near-term, clinically-defined infection syndromes (sepsis, meningitis, and pneumonia), excluding major congenital abnormalities. Clinical management was abstracted from hospital inpatient case notes (verification) which was considered as the gold standard against which to validate accuracy of women's report. Exit surveys were conducted using questions similar to The Demographic and Health Surveys (DHS) approach for coverage of childhood pneumonia treatment. We compared survey-report to case note verified, pooled across the five sites using random effects meta-analysis.A total of 1015 inpatient neonates admitted in the five hospitals met inclusion criteria with clinically-defined infection syndromes. According to case note verification, 96.7% received an injectable antibiotic, although only 14.5% of them received the recommended course of at least 7 days. Among women surveyed (n = 910), 98.8% (95% CI: 97.8-99.5%) correctly reported their baby was admitted to a neonatal ward. Only 47.1% (30.1-64.5%) reported their baby's diagnosis in terms of sepsis, meningitis, or pneumonia. Around three-quarters of women reported their baby received an injection whilst in hospital, but 12.3% reported the correct antibiotic name. Only 10.6% of the babies had a blood culture and less than 1% had a lumbar puncture.Women's report during exit survey consistently underestimated the denominator (reporting the baby had an infection), and even more so the numerator (reporting known injectable antibiotics). Admission to the neonatal ward was accurately reported and may have potential as a contact point indicator for use in household surveys, similar to institutional births. Strengthening capacity and use of laboratory diagnostics including blood culture are essential to promote appropriate use of antibiotics. To track quality of neonatal infection management, we recommend using inpatient records to measure specifics, requiring more research on standardised inpatient records.
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