Association of new sonographic features with outcome in neonates with necrotizing enterocolitis.

BACKGROUND: We have recently noted some sonographic features in necrotizing enterocolitis that have received little or no attention in the current literature. These include thickening of the mesentery, hyperechogenicity of intraluminal intestinal contents, abnormalities of the abdominal wall, and poor definition of the intestinal wall. It has been our impression that the above four sonographic findings are generally seen in neonates with more severe necrotizing enterocolitis and may be useful in predicting outcome. OBJECTIVES: The aim of this study is, firstly, to review a large series of neonates, known to have clinical NEC, to document how frequently the above four sonographic features occur in neonates with necrotizing enterocolitis and, secondly, to determine whether they are predictive of outcome. MATERIALS AND METHODS: We retrospectively analyzed the clinical, radiographic, sonographic, and surgical findings in neonates with necrotizing enterocolitis between 2018 and 2021. The neonates were categorized into two groups based on outcome. Group A included neonates with a favorable outcome defined as successful medical treatment with no surgical intervention. Group B included neonates with an unfavorable outcome defined as failed medical treatment requiring surgery (for acute complications or late strictures) or death because of necrotizing enterocolitis. The sonographic examinations were reviewed with attention to the features of mesenteric thickening, hyperechogenicity of intraluminal intestinal contents, abnormalities of the abdominal wall, and poor definition of the intestinal wall. We then determined the association of these four findings with the two groups. RESULTS: We included 102 neonates with clinical necrotizing enterocolitis: 45 in group A and 57 in group B. Neonates in group B were born at a significantly earlier gestational age (median 25 weeks, range 22-38 weeks) and had a significantly lower birth weight (median 715.5 g, range 404-3120 g) than those in group A (median age 32 weeks, range 22-39 weeks, p = 0.003; median weight 1190 g, range 480-4500 g, p = 0.002). The four sonographic features were present in both study groups but with different frequency. More importantly, all four were statistically significantly more frequently present in neonates in group B compared to group A: (i) mesenteric thickening, A = 31 (69%), B = 52 (91%), p = 0.007; (ii) hyperechogenicity of intestinal contents, A = 16 (36%), B = 41 (72%), p = 0.0005; (iii) abnormalities of the abdominal wall, A = 11 (24%), B = 35 (61%), p = 0.0004; and (iv) poor definition of the intestinal wall, A = 7 (16%), B = 25 (44%), p = 0.005. Furthermore, the proportion of neonates with more than two signs was greater in group B compared to group A (Z test, p < 0.0001, 95% CI = 0.22-0.61). CONCLUSION: The four new sonographic features described were found to occur statistically significantly more frequently in those neonates with an unfavorable outcome (group B) than in those with a favorable outcome (group A). The presence or absence of these signs should be included in the sonographic report to convey the radiologists concern regarding the severity of the disease in every neonate, suspected or known to have necrotizing enterocolitis, as the findings may impact further medical or surgical management.

Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19-a data-driven retrospective cohort study.

OBJECTIVES: To use national, pre- and post-pandemic electronic health records (EHR) to develop and validate a scenario-based model incorporating baseline mortality risk, infection rate (IR) and relative risk (RR) of death for prediction of excess deaths. DESIGN: An EHR-based, retrospective cohort study. SETTING: Linked EHR in Clinical Practice Research Datalink (CPRD); and linked EHR and COVID-19 data in England provided in NHS Digital Trusted Research Environment (TRE). PARTICIPANTS: In the development (CPRD) and validation (TRE) cohorts, we included 3.8 million and 35.1 million individuals aged ≥30 years, respectively. MAIN OUTCOME MEASURES: One-year all-cause excess deaths related to COVID-19 from March 2020 to March 2021. RESULTS: From 1 March 2020 to 1 March 2021, there were 127,020 observed excess deaths. Observed RR was 4.34% (95% CI, 4.31-4.38) and IR was 6.27% (95% CI, 6.26-6.28). In the validation cohort, predicted one-year excess deaths were 100,338 compared with the observed 127,020 deaths with a ratio of predicted to observed excess deaths of 0.79. CONCLUSIONS: We show that a simple, parsimonious model incorporating baseline mortality risk, one-year IR and RR of the pandemic can be used for scenario-based prediction of excess deaths in the early stages of a pandemic. Our analyses show that EHR could inform pandemic planning and surveillance, despite limited use in emergency preparedness to date. Although infection dynamics are important in the prediction of mortality, future models should take greater account of underlying conditions.

Junction Mapper is a novel computer vision tool to decipher cell-cell contact phenotypes.

Stable cell-cell contacts underpin tissue architecture and organization. Quantification of junctions of mammalian epithelia requires laborious manual measurements that are a major roadblock for mechanistic studies. We designed Junction Mapper as an open access, semi-automated software that defines the status of adhesiveness via the simultaneous measurement of pre-defined parameters at cell-cell contacts. It identifies contacting interfaces and corners with minimal user input and quantifies length, area and intensity of junction markers. Its ability to measure fragmented junctions is unique. Importantly, junctions that considerably deviate from the contiguous staining and straight contact phenotype seen in epithelia are also successfully quantified (i.e. cardiomyocytes or endothelia). Distinct phenotypes of junction disruption can be clearly differentiated among various oncogenes, depletion of actin regulators or stimulation with other agents. Junction Mapper is thus a powerful, unbiased and highly applicable software for profiling cell-cell adhesion phenotypes and facilitate studies on junction dynamics in health and disease.

Neonatal Morbidity Count Is Associated With a Reduced Likelihood of Achieving Recommendations for Protein, Lipid, and Energy in Very Low Birth Weight Infants: A Prospective Cohort Study.

BACKGROUND: Serious morbidity may elevate nutrient requirements and affect adherence to feeding guidelines for very low birth weight (VLBW) infants. An understanding of factors affecting nutrient intakes of VLBW infants will facilitate development of strategies to improve nutrient provision. Our aim was to examine the impact of neonatal morbidity count on achieving recommended nutrient intakes in VLBW infants. METHODS: VLBW infants enrolled in the Donor Milk for Improved Neurodevelopmental Outcomes trial (ISRCTN35317141, n = 363) were included. Serious morbidities and daily parenteral and enteral intakes were collected prospectively. RESULTS: Median intakes of infants with and without ≥1 morbidity met protein recommendations (3.5-4.5 g/kg/d) by week 2, although not maintained after week 4. Infants with ≥1 morbidity (vs without) were 2 weeks slower in achieving lipid (4.8-6.6 g/kg/d; week 4 vs 2) and energy (110-130 kcal/kg/d; week 5 vs 3) and 1 week slower in achieving carbohydrate recommendations (11.6-13.2 g/kg/d; week 4 vs 3). Adjusted hazard ratios of first achieving recommendations on any given day in infants with any 1 or 2 morbidities were 0.6 (95% confidence interval [CI], 0.5-0.9) and 0.6 (0.4-0.9), respectively, for protein; 0.5 (0.4-0.7) and 0.3 (0.2-0.5) for lipid; and 0.5 (0.4-0.7) and 0.3 (0.2-0.4) for energy. CONCLUSION: Morbidity is associated with a decreased likelihood of achieving lipid and consequently energy recommendations. This and the decline in protein intakes after the early neonatal period require further investigation to ensure optimal nutrition in this vulnerable population.

Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study.

BACKGROUND: Gaps in the diagnostic capacity and heterogeneity of national surveillance and reporting standards in Europe make it difficult to contain carbapenemase-producing Enterobacteriaceae. We report the development of a consistent sampling framework and the results of the first structured survey on the occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in European hospitals. METHODS: National expert laboratories recruited hospitals with diagnostic capacities, who collected the first ten carbapenem non-susceptible clinical isolates of K pneumoniae or E coli and ten susceptible same-species comparator isolates and pertinent patient and hospital information. Isolates and data were relayed back to national expert laboratories, which made laboratory-substantiated information available for central analysis. FINDINGS: Between Nov 1, 2013, and April 30, 2014, 455 sentinel hospitals in 36 countries submitted 2703 clinical isolates (2301 [85%] K pneumoniae and 402 (15%) E coli). 850 (37%) of 2301 K pneumoniae samples and 77 (19%) of 402 E coli samples were carbapenemase (KPC, NDM, OXA-48-like, or VIM) producers. The ratio of K pneumoniae to E coli was 11:1. 1·3 patients per 10 000 hospital admissions had positive clinical specimens. Prevalence differed greatly, with the highest rates in Mediterranean and Balkan countries. Carbapenemase-producing K pneumoniae isolates showed high resistance to last-line antibiotics. INTERPRETATION: This initiative shows an encouraging commitment by all participants, and suggests that challenges in the establishment of a continent-wide enhanced sentinel surveillance for carbapenemase-producing Enterobacteriaeceae can be overcome. Strengthening infection control efforts in hospitals is crucial for controlling spread through local and national health care networks. FUNDING: European Centre for Disease Prevention and Control.

XperimentR: painless annotation of a biological experiment for the laboratory scientist.

BACKGROUND: Today's biological experiments often involve the collaboration of multidisciplinary researchers utilising several high throughput 'omics platforms. There is a requirement for the details of the experiment to be adequately described using standardised ontologies to enable data preservation, the analysis of the data and to facilitate the export of the data to public repositories. However there are a bewildering number of ontologies, controlled vocabularies, and minimum standards available for use to describe experiments. There is a need for user-friendly software tools to aid laboratory scientists in capturing the experimental information. RESULTS: A web application called XperimentR has been developed for use by laboratory scientists, consisting of a browser-based interface and server-side components which provide an intuitive platform for capturing and sharing experimental metadata. Information recorded includes details about the biological samples, procedures, protocols, and experimental technologies, all of which can be easily annotated using the appropriate ontologies. Files and raw data can be imported and associated with the biological samples via the interface, from either users' computers, or commonly used open-source data repositories. Experiments can be shared with other users, and experiments can be exported in the standard ISA-Tab format for deposition in public databases. XperimentR is freely available and can be installed natively or by using a provided pre-configured Virtual Machine. A guest system is also available for trial purposes. CONCLUSION: We present a web based software application to aid the laboratory scientist to capture, describe and share details about their experiments.

Arrhythmia associated with tetracaine in an extremely low birth weight premature infant.

Infants in NICUs undergo a variety of painful procedures. The management of pain has become an integral part of newborn infant care with the use of both systemic and topical agents to provide analgesia and anesthesia for procedural pain. Tetracaine and prilocaine-lidocaine are the 2 topical anesthetics most frequently used. Tetracaine belongs to an ester group of local anesthetics available as a topical 4% gel (Ametop, Smith and Nephew, Canada). The major side effects reported when using topical anesthetics are cutaneous reactions. There are no definite reports of systemic toxicity in the published literature. We present a recent case of an extremely low birth weight premature infant who developed a clinically significant arrhythmia after topical tetracaine was applied before the insertion of a peripherally inserted central catheter. The infant had no other identifiable cause for the resulting bradycardia that occurred only after Ametop was applied. The cardiac symptoms resolved with treatment. This case highlights a significant potential adverse event when using topical tetracaine.

Arginine can be synthesized from enteral proline in healthy adult humans.

There is considerable controversy recently in identifying dietary precursors for arginine synthesis. We have previously shown in human neonates and piglets that proline is the sole dietary precursor for arginine synthesis. It is unclear in adult humans whether proline is a dietary precursor for arginine. We performed a multi-tracer stable isotope study in adults using (15)N(2)-ureido arginine and (15)N proline to elucidate synthesis of citrulline and arginine and determine whether proline is a precursor for arginine. Primed, intermittent infusions of the labeled amino acids were given enterally to 5 healthy men consuming a standardized milkshake diet. Blood was sampled during plateau enrichment between 1.5 and 3 h. Plasma enrichment occurred for both tracers, giving enteral turnover estimates of 93 µmol · kg(-1) · h(-1) for arginine and 154 µmol · kg(-1) · h(-1) for proline. Appearance of the label from proline in arginine and the intermediaries, ornithine and citrulline, was measured in all participants. The rate of synthesis of arginine from proline was 3.7 µmol · kg(-1) · h(-1), which is estimated to be ~40% of newly synthesized arginine. In this first study in adult humans using an enteral proline tracer, we have demonstrated synthesis of arginine from this dietary amino acid. Therefore, as in newborns, proline must now be considered a dietary precursor for arginine in healthy adults.

Arginine synthesis from enteral glutamine in healthy adults in the fed state.

Recent studies have documented transfer of labeled nitrogen from [2-(15)N]glutamine to citrulline and arginine in fasting human adults. Conversely, in neonates and piglets we have shown no synthesis of arginine from [2-(15)N]glutamate, and others have shown in mice that glutamine is a nitrogen, but not a carbon donor, for arginine synthesis. Therefore, we performed a multitracer study to determine whether glutamine is a nitrogen and/or carbon donor for arginine in healthy adult men. Two glutamine tracers, 2-(15)N and 1-(13)C, were given enterally to five healthy men fed a standardized milkshake diet. There was no difference in plasma enrichments between the two glutamine tracers. 1-(13)C isotopomers of citrulline and arginine were synthesized from [1-(13)C]glutamine. Three isotopomers each of citrulline and arginine were synthesized from the [2-(15)N]glutamine tracer: 2-(15)N, 5-(15)N, and 2,5-(15)N(2). Significantly greater enrichment was found of both [5-(15)N]arginine (0.75%) and citrulline (3.98%) compared with [2-(15)N]arginine (0.44%) and [2-(15)N]citrulline (2.62%), indicating the amino NH(2) from glutamine is mostly transferred to arginine and citrulline by transamination. Similarly, the enrichment of the 1-(13)C isotopomers was significantly less than the 2-(15)N isotopomers, suggesting rapid formation of α-ketoglutarate and recycling of the nitrogen label. Our results show that the carbon for 50% of newly synthesized arginine comes from dietary glutamine but that glutamine acts primarily as a nitrogen donor for arginine synthesis. Hence, studies using [2-(15)N]glutamine will overestimate arginine synthesis rates.

Arginine is synthesized from proline, not glutamate, in enterally fed human preterm neonates.

In neonatal mammals, arginine is synthesized in the enterocyte, with either proline or glutamate as the dietary precursor. We have shown several times in piglets that proline is the only precursor to arginine, although in vitro evidence supports glutamate in this role. Because of this uncertainty, we performed a multitracer stable isotope study to determine whether proline, glutamate, or both are dietary precursors for arginine in enterally fed human neonates. Labeled arginine (M + 2), proline (M + 1), and glutamate (M + 3) were given enterally to 15 stable, growing preterm infants (GA at birth 30-35 wk) at 1-3 wk postnatal age. Enrichment in urine of the tracer amino acids and the M + 1 and M + 3 isotopomers of arginine were measured by LC-tandem mass spectrometry to determine the contribution of proline and glutamate to arginine synthesis. Plateau enrichments of arginine and proline tracers were measurable in urine. Urinary glutamate enrichment was not detected. Conversion of proline to arginine was detected. However, the M + 3 isotopomer of arginine, which would have been synthesized from glutamate, was not detected. We conclude that, in contrast to the current consensus in the literature based on in vitro studies, proline is the major contributor to arginine synthesis in human preterm infants.

Trends in cause-specific mortality at a Canadian outborn NICU.

OBJECTIVE: To retrospectively review changes in the causes of death of infants dying in the NICU at Canada's largest outborn pediatric center. PATIENTS AND METHODS: All inpatient deaths at the Hospital for Sick Children's NICU that occurred in the years 1997, 2002, and 2007 were retrospectively reviewed to identify the primary cause of death. Classification of the cause of death was based on a modified version of the Perinatal Society of Australia and New Zealand's Neonatal Death Classification. RESULTS: The annual mortality rate remained relatively constant (average of 7.6 deaths per 100 admissions between 1988 and 2007). A total of 156 deaths were analyzed: 53 in 1997; 50 in 2002; and 53 in 2007. The chronological age at which premature infants died increased significantly over the 3 time periods (P = .01). The proportion of deaths attributable to extreme prematurity and intraventricular hemorrhage decreased over the study period, whereas the proportion of deaths attributed to gastrointestinal causes (specifically necrotizing enterocolitis and focal intestinal perforation) increased. The proportion of infants for whom there was a decision to limit care before death was stable at between 83% and 92%. CONCLUSIONS: A larger proportion of outborn premature infants admitted to the Hospital for Sick Children's NICU seem to be surviving the early problems of prematurity only to succumb to late complications.

The significance of d-isomers in stable isotope studies in humans is dependent on the age of the subject and the amino acid tracer.

d-Amino acids (d-AAs) in stable isotope tracers may result in erroneous estimates of enrichment, particularly if urine is used as a surrogate for plasma enrichment. Previous studies suggest that a d-AA content of less than 0.2% will not result in significant error in studies with adult humans. To describe the effects of d-AA content of less than 0.2%, in 3 different AA tracers, on isotope enrichment in urine and plasma, arginine, proline, and phenylalanine (Phe) tracers were given enterally to human neonates. Enrichment was measured in urine and plasma using chiral chromatography and tandem mass spectrometry. The Phe tracer was also given parenterally to human neonates and enterally to children and adults to further characterize the d-AA effect. All isotopes had a confirmed d-AA content of less than 0.2%. Labeled d-arginine resulted in an overestimate for enrichment of 20% in plasma and 87% in urine. A smaller effect was seen for d-Phe, which resulted in a 5% overestimate for plasma and 40% in urine. d-Proline had no significant effect. Using the same Phe tracer, a developmental effect was found, with a reduction in the overestimate in children compared with infants and no effect on enrichment in adults. Investigators using commercially produced, stable isotope-labeled AAs need to be aware that there is no safe level of d contamination; a d-AA content less than 0.2% may result in significant overestimate for enrichment, even in plasma, for infants and children. This source of error can be avoided by the use of chiral chromatography.

MiMiR--an integrated platform for microarray data sharing, mining and analysis.

BACKGROUND: Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. RESULTS: A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. CONCLUSION: The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.