A Curvature-Enhanced Random Walker Segmentation Method for Detailed Capture of 3D Cell Surface Membranes.

High-resolution 3D microscopy is a fast advancing field and requires new techniques in image analysis to handle these new datasets. In this work, we focus on detailed 3D segmentation of Dictyostelium cells undergoing macropinocytosis captured on an iSPIM microscope. We propose a novel random walker-based method with a curvature-based enhancement term, with the aim of capturing fine protrusions, such as filopodia and deep invaginations, such as macropinocytotic cups, on the cell surface. We tested our method on both real and synthetic 3D image volumes, demonstrating that the inclusion of the curvature enhancement term can improve the segmentation of the aforementioned features. We show that our method performs better than other state of the art segmentation methods in 3D images of Dictyostelium cells, and performs competitively against CNN-based methods in two Cell Tracking Challenge datasets, demonstrating the ability to obtain accurate segmentations without the requirement of large training datasets. We also present an automated seeding method for microscopy data, which, combined with the curvature-enhanced random walker method, enables the segmentation of large time series with minimal input from the experimenter.

QuimP: analyzing transmembrane signalling in highly deformable cells.

Summary: Transmembrane signalling plays important physiological roles, with G protein-coupled cell surface receptors being particularly important therapeutic targets. Fluorescent proteins are widely used to study signalling, but analyses of image time series can be challenging, in particular when cells change shape. QuimP software semi-automatically tracks spatio-temporal patterns of fluorescence at the cell membrane at high spatial resolution. This makes it a unique tool for studying transmembrane signalling, particularly during cell migration in immune or cancer cells for example. Availability and implementation: QuimP (http://warwick.ac.uk/quimp) is a set of Java plugins for Fiji/ImageJ (http://fiji.sc) installable through the Fiji Updater (http://warwick.ac.uk/quimp/wiki-pages/installation). It is compatible with Mac, Windows and Unix operating systems, requiring version >1.45 of ImageJ and Java 8. QuimP is released as open source (https://github.com/CellDynamics/QuimP) under an academic licence. Supplementary information: Supplementary data are available at Bioinformatics online.

Image based modeling of bleb site selection.

Cells often employ fast, pressure-driven blebs to move through tissues or against mechanical resistance, but how bleb sites are selected and directed to the cell front remains an open question. Previously, we found that chemotaxing Dictyostelium cells preferentially bleb from concave regions, where membrane tension facilitates membrane-cortex detachment. Now, through a novel modeling approach based on actual cell contours, we use cell geometry to predict where blebs will form in migrating cells. We find that cell geometry alone, and by implication, physical forces in the membrane, is sufficient to predict the location of blebs in rounded cells moving in a highly resistive environment. The model is less successful with more polarized cells moving against less resistance, but can be greatly improved by positing a front-to-back gradient in membrane-cortex adhesion. In accord with this prediction, we find that Talin, which links membrane and cortex, forms such a front-to-back gradient. Thus our model provides a means of dissecting out the role of physical forces in controlling where blebs form, and shows that in certain circumstances they could be the major determining factor.

A.S.P.E.N. position paper: Clinical role for alternative intravenous fat emulsions.

The currently available, standard soybean oil (SO)-based intravenous fat emulsions (IVFEs) meet the needs of most parenteral nutrition (PN) patients. There are alternative oil-based fat emulsions, such as medium-chain triglycerides (MCTs), olive oils (OOs), and fish oils (FOs), that, based on extensive usage in Europe, have an equivalent safety profile to SO. These alternative IVFEs are metabolized via different pathways, which may lead to less proinflammatory effects and less immune suppression. These alternative oil-based IVFEs are not currently available in the United States. Many patients who require IVFEs are already in a compromised state. Such patients could potentially have better clinical outcomes when receiving one of the alternative IVFEs to diminish the intake of the potentially proinflammatory ω-6 fatty acid-linoleic acid-which comprises more than 50% of the fatty acid profile in SO. Further research is needed on these alternative oil-based IVFEs to identify which IVFE oils or which combination of oils may be most clinically useful for specific patient populations.

Persistent alanine aminotransferase elevations in children with parenteral nutrition-associated liver disease.

BACKGROUND: Parenteral nutrition-associated liver disease (PNALD) is a serious condition affecting many children with short bowel syndrome. The aim of this study was to longitudinally assess serum alanine aminotransferase (ALT), a marker for hepatocyte injury, in enterally fed children with PNALD. METHODS: Retrospective chart review of 31 patients treated from 1999 to 2006 by the Center for Advanced Intestinal Rehabilitation at Children's Hospital Boston (Mass). Inclusion criteria included PN duration of greater than 3 months with subsequent tolerance of full enteral nutrition and evidence of PN-associated liver injury. Time to normalize ALT and direct bilirubin were estimated using Kaplan-Meier and Cox proportional hazards methods. RESULTS: Mean age PN cessation was 6 months (range, 2-14 months). Median PN duration was 18 weeks (interquartile range [IQR], 13-33 weeks), and median follow-up was 24 weeks (IQR, 14-48 weeks). After transition to full enteral nutrition, 74% of children normalized direct bilirubin, whereas only 50% normalized ALT. Kaplan-Meier median time to direct bilirubin and ALT normalization were 13 weeks and 35 weeks, respectively (P = .001). CONCLUSION: Children with PNALD who have achieved PN independence have persistent ALT elevation despite normal direct bilirubin levels. This implies that hepatic injury may be ongoing beyond the time of bilirubin normalization in this cohort of patients.

Growth and nutritional status in infants with short-bowel syndrome after the serial transverse enteroplasty procedure.

BACKGROUND & AIMS: The aim of this study was to describe the long-term nutritional outcomes of 4 patients with short bowel syndrome (SBS) who underwent a newly described bowel-lengthening procedure, the serial transverse enteroplasty (STEP) procedure. METHODS: We performed a retrospective review of the medical records of 4 children who underwent STEP at 1 center. The primary outcome measure was the percentage of total dietary energy received by the enteral route before and after STEP. Other outcome measures were weight and height Z scores and body composition, as measured by arm anthropometric values. RESULTS: Four children with SBS were identified, all of whom had been dependent on parenteral nutrition since birth. The mean preoperative follow-up period was 234 days (range, 63-502 days), and the mean postoperative follow-up period was 362 days (range, 252-493 days). By using model-based mean estimates, the mean enteral nutrition intake was 48% preoperatively vs 62% postoperatively (P = .02). The model mean weight for age Z score increased by .7 SDs postoperatively (P = .01), and the model mean weight for height increased by .6 SDs (P < .0001). The percent standard mid-upper-arm circumference increased by 13.1% postoperatively (P = .03), and the percent standard triceps skinfold increased by 24.5% postoperatively (P < .0001). CONCLUSIONS: The STEP procedure was associated with improved growth and body composition among 4 children with SBS in the face of a decreasing need for parenteral nutrition. Among patients with refractory SBS and dilated small intestine, the STEP procedure is associated with improved clinical and nutritional outcomes in the first year after surgery.

Reversal of parenteral nutrition-associated liver disease in two infants with short bowel syndrome using parenteral fish oil: implications for future management.

Here we report the reversal of cholestasis in 2 infants with intestinal failure and parenteral nutrition-associated liver disease. Treatment involved the substitution of a conventional intravenous fat emulsion with one containing primarily omega-3 fatty acids. Biochemical tests of liver function improved significantly. One child was removed from the liver transplantation list because of improved hepatic function, and the second child had complete resolution of cholestasis while solely on parenteral nutrition. This suggests that fat emulsions made from fish oils may be an effective means of treating and preventing this often-fatal condition. A randomized, controlled trial is necessary to study the efficacy of this new approach to parenteral nutrition-associated liver disease.

The role of enteral nutrition in the reversal of parenteral nutrition-associated liver dysfunction in infants.

BACKGROUND: Liver dysfunction in children dependent on parenteral nutrition (PN) is well established, and the extent of hyperbilirubinemia has been shown to correlate with morbidity and mortality. The aim of this study was to assess whether increasing provisions of enteral nutrition can improve PN-associated hyperbilirubinemia over time. METHODS: A retrospective review was conducted on infants in our institution's Short Bowel Syndrome Clinic from 1999 to 2004. Inclusion criteria included PN duration more than 1 month, serum direct bilirubin more than 3 mg/dL while on PN, and tolerance of full enteral nutrition with eventual discontinuation of PN. Paired t tests were used for statistical analyses. RESULTS: Twelve infants were identified with a PN duration of 5 +/- 1 months. Five patients underwent liver biopsy while on PN, and histological evidence of cholestasis was found on all specimens. Peak total and direct bilirubin levels were 10.5 +/- 1.9 and 7.0 +/- 1.6 mg/dL, respectively, and occurred at time of PN discontinuation. Only 2 patients had improvement in serum bilirubin levels before initiation of full enteral nutrition. After initiation of full enteral nutrition and discontinuation of PN, all patients achieved permanent normalization of bilirubin levels by 4 months (P < .05) after a 1-month plateau phase. Alkaline phosphatase levels approached reference range within this time but were not significant. CONCLUSION: These data demonstrate for the first time that although PN-dependent infants can achieve normalization of marked hyperbilirubinemia with enteral nutrition, the improvement in liver function usually begins only after full enteral nutrition is tolerated and PN is withdrawn. These findings support the aggressive weaning of PN to enteral nutrition in infants with short bowel syndrome.

Glutamine supplementation in infants with gastrointestinal disease: a randomized, placebo-controlled pilot trial.

OBJECTIVE: Glutamine (Gln) is a non-essential amino acid that plays an important role in energy metabolism for gastrointestinal epithelia and other cells with rapid turnover. We evaluated the effects of enteral supplementation with Gln in infants undergoing surgery for congenital or acquired gastrointestinal disease. METHODS: This was a randomized, double-masked, controlled clinical trial. RESULTS: Twenty infants were randomly assigned to receive Gln (n = 9) or placebo amino acid (n = 11), with a goal of supplemental amino acid intake of 0.4 g.kg(-1).d(-1). Infants were weaned from parenteral nutrition, and enteral feeds were started according to a standardized feeding protocol. Median (interquartile range) durations of parenteral nutrition were 39 d (12 to 99) in the Gln group and 21 d (6 to 59) in the control group (P = 0.201). Median (interquartile range) durations needed to reach 80% of the US recommended dietary allowance for energy with enteral nutrition were 24 d (8 to 55) in the Gln group and 12.5 d (5 to 32) in the control group (P = 0.313). There were no differences in the occurrence of infections between groups. Among all infants enrolled, significant correlations were found between duration of parenteral nutrition and residual small bowel length, peak concentrations of direct bilirubin, and alanine aminotransferase. Peak direct bilirubin was associated with longer duration of parenteral nutrition, shorter gestation, older age before feeds were started, shorter bowel length, and larger amounts of parenteral energy and protein intake. CONCLUSIONS: In this pilot trial, enteral Gln supplementation was well tolerated among infants with surgical gastrointestinal disease. There was no effect observed on the duration of parenteral nutrition, tolerance of enteral feeds, or intestinal absorptive or barrier function. Larger, multicenter trials in infants with surgical gastrointestinal disease are needed due to the variability in important outcome measurements.

Nutrition for the pediatric office: update on vitamins, infant feeding and food allergies.

PURPOSE OF REVIEW: Advances in the field of pediatric nutrition continue to help the pediatric office practitioner provide excellent clinical care to their patients. In 2003, several important papers were published in the field of clinical nutrition that are reviewed. RECENT FINDINGS: New recommendations by the American Academy of Pediatrics for vitamin D supplementation for breast-fed infants have been published that underscore the importance of routine supplementation with 200 IU vitamin D per day. Vitamin K should be provided (0.5 to 1 mg intramuscularly) to all newborns. The authors also review original reports evaluating the role of long-chain polyunsaturated fatty acids in infant formulas, the duration of exclusive breast-feeding, and the natural history of food allergies. Some observational studies support exclusive breast-feeding for 6 months. Data concerning the efficacy of long-chain polyunsaturated fatty acids are conflicting but do support the safety of these additives. SUMMARY: Regular supplementation with vitamin D, and newborn provision of vitamin K, are important nutritional interventions for infants and children.

Update on pediatric nutrition: breastfeeding, infant nutrition, and growth.

Recent studies continue to point out the critical nature of a patient's nutritional status in helping to determine important health outcomes in pediatrics. We review recent data concerning the composition of breast milk and its adequacy to support infant growth in the first six months of life, as well as trials that support breastfeeding as an important method to delay or reduce the incidence of atopic diseases such as eczema, allergies, and asthma. Studies have also been published that show how physician education and training about breastfeeding can be optimized. Studies showing how nutritional status is measured (using standard anthropometric techniques as well as more modern measures of basal metabolic rate) are highlighted, as well as the role of micronutrient supplementation of patients with the human immunodeficiency virus infection and diarrheal diseases.

Effectiveness of a clinical practice guideline for parenteral nutrition: a 5-year follow-up study in a pediatric teaching hospital.

OBJECTIVE: To determine the effectiveness of a clinical practice guideline (CPG) on the use of parenteral nutrition (PN) at a tertiary care pediatric hospital. METHODS: Review of prospectively collected data on hospital-wide PN use 2 years before and 5 years after the establishment of the CPG. Effectiveness of the CPG was measured as the percentage of PN courses lasting fewer than 5 days and the number of PN starts per 1000 patient days. RESULTS: During the study period, 5745 PN courses were administered. The mean (SD) number of PN starts per 1000 inpatient days was 8.86 (0.78) before the CPG and 9.54 (2.49) afterwards (p = .28). The percentage courses of PN lasting for fewer than 5 days declined from 26.3% before the CPG to 18.4% afterwards (p < .0001). A multivariate model confirmed that the rate of short-term PN starts declined after the CPG was issued. The mean (SD) number of PN courses shorter than 5 days in the 2 years before the CPG was 2.33 (0.42) per 1000 patient days versus 1.75 (0.45) in the 5 years after the CPG was instituted (p = .005), which is a 25% decline. The services with the highest volume of PN use showed the most significant decreases in short-term PN use. A cost savings to the hospital of more than $50,000 may have been realized. CONCLUSIONS: In a large pediatric tertiary care hospital, a CPG was successfully deployed. CPGs can favorably affect the use rates and costs of parenteral nutrition.