Open-source Software Sustainability Models: Initial White Paper From the Informatics Technology for Cancer Research Sustainability and Industry Partnership Working Group.

BACKGROUND: The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term sustainability of the software being developed by ITCR grantees. To address this challenge, the ITCR sustainability and industry partnership working group (SIP-WG) was convened in 2019. OBJECTIVE: The charter of the SIP-WG is to investigate options to enhance the long-term sustainability of the OSS being developed by ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The working group assembled models from the ITCR program, from other studies, and from the engagement of its extensive network of relationships with other organizations (eg, Chan Zuckerberg Initiative, Open Source Initiative, and Software Sustainability Institute) in support of this objective. METHODS: This paper reviews the existing sustainability models and describes 10 OSS use cases disseminated by the SIP-WG and others, including 3D Slicer, Bioconductor, Cytoscape, Globus, i2b2 (Informatics for Integrating Biology and the Bedside) and tranSMART, Insight Toolkit, Linux, Observational Health Data Sciences and Informatics tools, R, and REDCap (Research Electronic Data Capture), in 10 sustainability aspects: governance, documentation, code quality, support, ecosystem collaboration, security, legal, finance, marketing, and dependency hygiene. RESULTS: Information available to the public reveals that all 10 OSS have effective governance, comprehensive documentation, high code quality, reliable dependency hygiene, strong user and developer support, and active marketing. These OSS include a variety of licensing models (eg, general public license version 2, general public license version 3, Berkeley Software Distribution, and Apache 3) and financial models (eg, federal research funding, industry and membership support, and commercial support). However, detailed information on ecosystem collaboration and security is not publicly provided by most OSS. CONCLUSIONS: We recommend 6 essential attributes for research software: alignment with unmet scientific needs, a dedicated development team, a vibrant user community, a feasible licensing model, a sustainable financial model, and effective product management. We also stress important actions to be considered in future ITCR activities that involve the discussion of the sustainability and licensing models for ITCR OSS, the establishment of a central library, the allocation of consulting resources to code quality control, ecosystem collaboration, security, and dependency hygiene.

Perturbation-Based Balance Training Using Repeated Trips on a Walkway vs. Belt Accelerations on a Treadmill: A Cross-Over Randomised Controlled Trial in Community-Dwelling Older Adults.

Background: Walkway and treadmill induced trips have contrasting advantages, for instance walkway trips have high-ecological validity whereas belt accelerations on a treadmill have high-clinical feasibility for perturbation-based balance training (PBT). This study aimed to (i) compare adaptations to repeated overground trips with repeated treadmill belt accelerations in older adults and (ii) determine if adaptations to repeated treadmill belt accelerations can transfer to an actual trip on the walkway. Method: Thirty-eight healthy community-dwelling older adults underwent one session each of walkway and treadmill PBT in a randomised crossover design on a single day. For both conditions, 11 trips were induced to either leg in pseudo-random locations interspersed with 20 normal walking trials. Dynamic balance (e.g., margin of stability) and gait (e.g., step length) parameters from 3D motion capture were used to examine adaptations in the walkway and treadmill PBT and transfer of adaptation from treadmill PBT to a walkway trip. Results: No changes were observed in normal (no-trip) gait parameters in both training conditions, except for a small (0.9 cm) increase in minimum toe elevation during walkway walks (P < 0.01). An increase in the margin of stability and recovery step length was observed during walkway PBT (P < 0.05). During treadmill PBT, an increased MoS, step length and decreased trunk sway range were observed (P < 0.05). These adaptations to treadmill PBT did not transfer to a walkway trip. Conclusions: This study demonstrated that older adults could learn to improve dynamic stability by repeated exposure to walkway trips as well as treadmill belt accelerations. However, the adaptations to treadmill belt accelerations did not transfer to an actual trip. To enhance the utility of treadmill PBT for overground trip recovery performance, further development of treadmill PBT protocols is recommended to improve ecological authenticity.

Endoscopic Reduction of Sigmoid Volvulus in a 15-Year-Old Male.

Sigmoid volvulus is a well-recognized phenomenon in the elderly but rare in children. The proposed mechanism involves rotation of a redundant sigmoid loop around a narrow, elongated mesentery with subsequent vascular occlusion. The condition can be intermittent or may resolve spontaneously, complicating diagnosis. Early diagnosis is imperative to prevent ischemic complications including necrosis, perforation, and sepsis. Abdominal pain, abdominal distention, and vomiting are the most common presenting symptoms, however abdominal tenderness is uncommon. Colonic dilation is the most frequent finding on abdominal radiograph. Contrast enema reveals a "bird's beak" configuration of the twisted colon and moreover, is successful in reducing the majority of pediatric cases. If there is no evidence of bowel ischemia or perforation, endoscopic reduction has been proposed as first-line treatment for sigmoid volvulus, especially in children. We report the case of 15-year-old male in which endoscopic reduction of sigmoid volvulus was successful without complication.

Using Queue Theory and Load-Leveling Principles to Identify a Simple Metric for Resource Planning in a Pediatric Emergency Department.

Increased waiting time in pediatric emergency departments is a well-recognized and complex problem in a resource-limited US health care system. Efforts to reduce emergency department wait times include modeling arrival rates, acuity, process flow, and human resource requirements. The aim of this study was to investigate queue theory and load-leveling principles to model arrival rates and to identify a simple metric for assisting with determination of optimal physical space and human resource requirements. We discovered that pediatric emergency department arrival rates vary based on time of day, day of the week, and month of the year in a predictable pattern and that the hourly change in pediatric emergency department waiting room census may be useful as a simple metric to identify target times for shifting resources to better match supply and demand at no additional cost.

20-year-old man • sudden-onset chest pain • worsening pain with cough and exertion • Dx?

► Sudden-onset chest pain ► Worsening pain with cough and exertion ► No improvement with naproxen.

Patient Satisfaction Surveys in the Outpatient Clinic Setting: The Variability of Response With Positively or Negatively Toned Questions.

The purpose of this study was to determine whether a patient satisfaction survey in the outpatient clinic setting using questions with either a positive or negative tone would produce consistent responses. This was a prospective study using a 20-question paper survey delivered to medical students who were asked to rate on a scale of 1 to 10 to what degree they either agree or disagree with statements regarding their most recent personal outpatient clinic health care visit (any medical specialty). The same survey was administered again through an e-mail link 1 week later. One hundred fifty (77%) students completed the 20-item survey and 53 (35%) of the participating students completed the follow-up e-mail survey. Seven of the 10 question pairs on the paper survey revealed statistically significant differences in responses based on tone, with greater values for disagreement with negatively toned questions than values representing agreement with positive-toned questions. The match rates for similar questions posed on the paper survey and then the e-mail survey 1 week later ranged between 27.8% and 56.6%. This study demonstrated that, with an outpatient health care patient satisfaction survey, disagreement with a negative-toned question was stronger than agreement with a positive-toned question. There was poor correlation between survey responses when first posed on a paper survey and then repeated on a digital survey 1 week later. These findings suggest that the wording of survey questions may affect responses and that survey answers change with time and across delivery platforms.

Utility of Esophagogastroduodenoscopy in the Evaluation of Uncomplicated Abdominal Pain in Children.

Esophagogastroduodenoscopy (EGD) is commonly performed for abdominal pain in children, and in the presence of alarm symptoms, the diagnostic yield of this procedure is high. The aim of this study was to investigate the utility of EGD when performed for uncomplicated abdominal pain in children in the absence of alarm symptoms. Charts of all children less than 18 years of age who underwent EGD at the University of Florida between January 2016 and October 2018 were reviewed. Of 1478 children who underwent EGD for any indication, 287 patients (male-to-female = 123:164) were discovered to have undergone EGD, in the absence of colonoscopy, for uncomplicated acute or chronic abdominal pain, nausea, vomiting, gastroesophageal reflux, and/or dyspepsia, with no alarm symptoms. A significant change in clinical management was noted in 20 (7.0%) children. The findings of this procedure changed clinical management in a minority of our study participants.

Liver transplantation in children with metabolic diseases: the studies of pediatric liver transplantation experience.

Metabolic diseases are the second largest indication for LT in children after BA. There are limited data on the long-term post-transplant outcome in this unique group of patients. Therefore, our aim was to assess post-liver transplant outcomes and to evaluate risk factors for mortality and graft loss in children with metabolic disorders in comparison to those with non-metabolic diagnoses. We reviewed all patients enrolled in the SPLIT registry. Between 1995 and 2008, 446 of 2997 (14.9%) children enrolled in SPLIT underwent liver transplant for metabolic diseases. One-yr and five-yr patient survival for children with metabolic diseases was 94.6% and 88.9% and for those with other diseases 90.7% and 86.1% (log-rank p = 0.05), respectively. One-yr and five-yr graft survival for children with metabolic disorders was 90.8% and 83.8%, and for those with other diseases 85.4% and 78.0% (log-rank p = 0.005), respectively. Children with metabolic diseases were less likely to experience gastrointestinal complications (5.6% vs. 10.7%, p = 0.001), portal vein thrombosis (2.9% vs. 5.2%, p = 0.04), and reoperations within 30 days post-transplant (33.4% vs. 37.8%, p = 0.05) than those with other indications. In conclusion, children who underwent liver transplant for metabolic disease had similarly excellent patient survival as, and better graft survival than, those who received a liver allograft for other indications.

Antibodies to CBir1 are associated with glycogen storage disease type Ib.

OBJECTIVES: : Glycogen storage disease (GSD) type Ib is a congenital disorder of glycogen metabolism that is associated with neutropenia, neutrophil and monocyte dysfunction, and an inflammatory bowel disease (IBD) that mimics a Crohn disease phenotype. The enteric microflora is implicated in the pathogenesis of IBD; however, its role in the development of GSD-associated IBD is unknown. Antibody reactivity to Saccharomyces cerevisiae antibodies (ASCA), Escherichia coli outer membrane porin C (anti-OmpC), and bacterial flagellin (anti-CBir1) have been associated with Crohn disease in the general population, but they have an undetermined association in children and adults with GSD-Ib. Our goal was to examine the association of ASCA, anti-OmpC, and anti-CBir1 with the clinical features of GSD-Ib enterocolitis. PATIENTS AND METHODS: : A retrospective review identified 19 patients with GSD-Ib with or without a known diagnosis of enterocolitis. Radiographic, endoscopic, and serologic data were collected and assays for ASCA, anti-OmpC, and anti-CBir1 obtained. RESULTS: : Seven patients had combined radiographic, endoscopic, and histologic evidence of intestinal inflammation; the majority had ileocolonic involvement. Seventeen of 19 (89%) patients had elevated anti-CBir1 levels (6/7 in the IBD group and 11/12 in the no clinical evidence of IBD group). Thirteen of 19 (68%) had elevated anti-OmpC levels (5/7 in the IBD group and 8/12 in the no clinical evidence of IBD group). Eleven of 19 (58%) patients had elevated ASCA IgA levels (4/7 in the IBD group and 7/12 in the no clinical evidence of IBD group). CONCLUSIONS: : Nearly all of the patients with GSD-Ib had elevated anti-CBir1 levels. The antibody did not differentiate those with and without a diagnosis of GSD-Ib-associated IBD. Seroreactivity to flagellin may represent immune dysfunction rather than active enterocolitis in this patient population. Long-term follow-up of the group without known IBD is required to determine whether these antibodies can predict intestinal inflammation.

Liver transplantation in children with glycogen storage disease: controversies and evaluation of the risk/benefit of this procedure.

GSD-I, III, and IV are congenital disorders of glycogen metabolism that are commonly associated with severe liver disease. Liver transplantation has been proposed as a therapy for these disorders. While liver transplantation corrects the primary hepatic enzyme defect, the extrahepatic manifestations of GSD often complicate post-transplantation management. Upon review of the English-language literature, 42 children <19 yr of age were discovered to have undergone liver transplantation for complications associated with GSD (18 patients with GSD-Ia, six with GSD-Ib, one with GSD-III, 17 with GSD-IV). An additional two children followed at our institution have undergone liver transplantation for GSD complications (one with GSD-Ia and one with GSD-III) and are included in this review. The risks and benefits of liver transplantation should be considered prior to performing liver transplantation in these metabolic disorders, particularly in GSD-Ia. As liver pathology is not the major source of morbidity in GSD-Ib and GSD-IIIa, liver transplantation should only be performed when there is high risk for HCC or evidence of substantial cirrhosis or liver dysfunction. Liver transplantation remains the best option for treatment of GSD-IV.

Antibodies to Escherichia coli outer membrane porin C in the absence of anti-Saccharomyces cerevisiae antibodies and anti-neutrophil cytoplasmic antibodies are an unreliable marker of Crohn disease and ulcerative colitis.

OBJECTIVES: Antibodies to Escherichia coli outer membrane porin C (anti-OmpC), Saccharomyces cerevisiae, and neutrophil-specific nuclear antigens are associated with inflammatory bowel disease (IBD) in children and young adults. We hypothesized that anti-OmpC, in the absence of anti-S cerevisiae antibodies (ASCA) and antineutrophil cytoplasmic antibodies (ANCA), is an assay that overestimates the presence of Crohn disease (CD) and ulcerative colitis (UC). PATIENTS AND METHODS: A retrospective review of patients evaluated at our institution between January 2002 and June 2006 revealed that 170 had serodiagnostic immunological assays performed as part of an evaluation for possible IBD. The assays were screened for a pattern in which anti-OmpC was present in the absence of ASCA and ANCA. RESULTS: Seven patients between 3 and 20 years of age were discovered to be positive for anti-OmpC but negative for ASCA and ANCA. These patients were determined to have significant medical conditions without combined radiographic, endoscopic, or histological evidence of IBD. Despite the reported 85% positive predictive value of anti-OmpC for IBD, none of the 7 patients with isolated anti-OmpC had a diagnosis of CD or UC. CONCLUSIONS: Anti-OmpC, in the absence of ASCA and ANCA, is a serological pattern noted in a subset of medically complex cases in children and young adults without CD or UC.

Critical thinking ability of associate, baccalaureate and RN-BSN senior students in Korea.

The purpose of this study was to compare the critical thinking ability of students enrolled in associate, baccalaureate, and Registered Nurse-Bachelor of Science in Nursing (RN-to-BSN) programs in Korea. The participants were 301 undergraduate nursing students. The instrument used for this study was the Watson & Glaser Critical Thinking Appraisal (WGCTA). The data were analyzed using descriptive statistics, t-test, and analysis of variance with Scheffe's multiple comparison. The average critical thinking ability score was 41.59. Bachelor of Science in Nursing (BSN) students scored significantly higher on critical thinking than the other 2 groups. Students < or = 22 years of age scored higher than the other age groups on critical thinking. This study provides preliminary evidence that the length and content of an educational program is as important as its focus on enabling students to develop their critical thinking abilities. This finding suggests a need to infuse critical thinking activities early in existing secondary school curricula as a way of encouraging students to develop their thinking abilities earlier.