PURPOSE:Complex pediatric surgery patients with thoracic tumors invading the mediastinum and infradiaphragmatic tumors extending into the chest are at risk for surgical morbidity and mortality if the patient's care is not coordinated. We sought to identify areas of focus when managing these patients to improve care.METHODS:A 20-year, retrospective study of pediatric patients with complex surgical pathology was performed. Demographic data, pre-operative characteristics, intraoperative data, complications, and outcomes data were collected. Three index cases were highlighted to provide granularity in patient management.RESULTS:Twenty-six patients were identified. Common pathology included mediastinal teratomas, foregut duplications, advanced Wilms tumors, hepatoblastoma, and lung masses. All cases were performed in a multidisciplinary fashion. All cases were done with pediatric cardiothoracic surgery and three cases (11.5%) required pediatric otolaryngology. Eight patients (30.7%) required cardiopulmonary bypass. Operative and 30-day mortality was zero.CONCLUSIONS:Management of complex pediatric surgical patients requires a multidisciplinary approach throughout the patient's hospital course. This multidisciplinary team should meet in advance of a patient's procedure to create a customized care plan that may include pre-operative optimization. At the time of their procedure, all necessary and emergency equipment should available. This approach improves patient safety and has resulted in excellent outcomes.LEVEL OF EVIDENCE:IV.

Background: Laparoscopic gastrostomy tube (GT) placement carries the risk of early tube dislodgement and is often modified with absorbable subcutaneously-tunneled transabdominal tacking sutures that can aid in tube replacement. However, these buried sutures may increase the risk of surgical site infection (SSI). This study sought to evaluate SSI rates associated with different types of transabdominal tacking sutures used in modified laparoscopic GT placement. Methods: A single-institution, retrospective review was performed of all patients <= 18 years-old undergoing modified laparoscopic GT placement between September 2016 and March 2020. Patients were stratified into three groups by suture type used, and the primary outcome was SSI within six weeks of surgery. Demographic and perioperative data were analyzed by chi-square or Fisher's exact test. Results: A total of 113 modified laparoscopic GT placements were performed at a median age of 9 months (interquartile range 3 months to 3 years). Prophylactic antibiotic use was similar between groups. Eleven patients (10%) developed an SSI, and all were treated with antibiotics alone. No SSIs were observed with the use of poliglecaprone suture (n = 46), and higher SSI rates were observed with use of polyglactin (n = 17) and polydioxanone (n = 51) suture (18% polyglactin vs. 16% polydioxanone vs. 0% poliglecaprone, p < 0.05). No differences were observed in rates of early postoperative dislodgement, leakage, or granulation tissue. Conclusion: Absorbable braided and long-lasting monofilament transabdominal tacking sutures may increase risk of SSI following modified laparoscopic gastrostomy tube placement. In this cohort, the use of poliglecaprone (Monocryl) suture was associated with no SSIs and similar rates of postoperative dislodgement, leakage, and granulation tissue. Published by Elsevier Inc.

Organisations conducting research programs often focus the work of their scientists and technologists on challenge problems (CPs). These challenges are designed to ensure that progress is measurable and relevant to the goals of the program sponsor. Generating and selecting pertinent CPs is difficult, as is assessing their value. We describe a method of generating and selecting CPs and its application in a highly collaborative, multi-organisation research program. Thirty-eight biologists, chemists, mathematicians and computer scientists across academic, commercial and government organisations generated and ranked their top choices from among 12 richly described candidate challenge problems. A ranked-choice voting formula was applied. Five CPs were highly scored; the remaining seven were distributed across a lower range of scores. The program sponsor subsequently directed researchers to address six CPs, including the elected five. Analysis of the rationales that participants offered for their CP rankings revealed four domain-independent dimensions of value: capability, speed, impact and synergy. These dimensions of value can help managers of interdisciplinary research programs systematically select a portfolio of CPs that will efficiently apply utilise resources towards program goals and facilitate measurement of scientific progress.

Most fault localization techniques take as input a faulty program, and produce as output a ranked list of suspicious code locations at which the program may be defective. When researchers propose a new fault localization technique, they typically evaluate it on programs with known faults. The technique is scored based on where in its output list the defective code appears. This enables the comparison of multiple fault localization techniques to determine which one is better. Previous research has evaluated fault localization techniques using artificial faults, generated either by mutation tools or manually. In other words, previous research has determined which fault localization techniques are best at finding artificial faults. However, it is not known which fault localization techniques are best at finding real faults. It is not obvious that the answer is the same, given previous work showing that artificial faults have both similarities to and differences from real faults. We performed a replication study to evaluate 10 claims in the literature that compared fault localization techniques (from the spectrum-based and mutation-based families). We used 2995 artificial faults in 6 real-world programs. Our results support 7 of the previous claims as statistically significant, but only 3 as having non-negligible effect sizes. Then, we evaluated the same 10 claims, using 310 real faults from the 6 programs. Every previous result was refuted or was statistically and practically insignificant. Our experiments show that artificial faults are not useful for predicting which fault localization techniques perform best on real faults. In light of these results, we identified a design space that includes many previously-studied fault localization techniques as well as hundreds of new techniques. We experimentally determined which factors in the design space are most important, using an overall set of 395 real faults. Then, we extended this design space with new techniques. Several of our novel techniques outperform all existing techniques, notably in terms of ranking defective code in the top-5 or top-10 reports.

Background: Low-magnitude, high-frequency vibration accelerates fracture and wound healing and prevents disuse atrophy in musculoskeletal tissues. Purpose: To investigate the role of low-magnitude, high-frequency vibration as a treatment to accelerate healing of an acute ligament injury and to examine gene expression in the intact Achilles tendon of the injured limb after low-magnitude, high-frequency vibration. Study Design: Controlled laboratory study. Methods: Complete surgical transection of the medial collateral ligament (MCL) was performed in 32 Sprague-Dawley rats, divided into control and low-magnitude, high-frequency vibration groups. Low-magnitude, high-frequency vibration started on postoperative day 2, and rats received vibration for 30 minutes a day for 12 days. All rats were sacrificed 2 weeks after the operation, and their intact and injured MCLs were biomechanically tested or used for histological analysis. Intact Achilles tendons from the injured limb were evaluated for differences in gene expression. Results: Mechanical testing revealed no differences in the ultimate tensile load or the structural stiffness between the control and vibration groups for either the injured or intact MCL. Vibration exposure increased gene expression of collagen 1 alpha (3-fold), interleukin 6 (7-fold), cyclooxygenase 2 (5-fold), and bone morphogenetic protein 12 (4-fold) in the intact Achilles tendon when compared with control tendons (P < .05). Conclusion: While no differences were observed in the mechanical or histological properties of the fully transected MCL after low-magnitude, high-frequency vibration treatment, significant enhancements in gene expression were observed in the intact Achilles tendon. These included collagen, several inflammatory cytokines, and growth factors critical for tendons. Clinical Relevance: As low-magnitude, high-frequency vibration had no negative effects on ligament healing, vibration therapy may be a useful tool to accelerate healing of other tissues (bone) in multitrauma injuries without inhibiting ligament healing. Additionally, the enhanced gene expression in response to low-magnitude, high-frequency vibration in the intact Achilles tendon suggests the need to further study its potential to accelerate tendon healing in partial injury or repair models.

Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10-9). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10-8), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD.

A previous meta-analysis of genome-wide association data by the Cohorts for Heart and Aging Research in Genomic Epidemiology and CKDGen consortia identified 16 loci associated with eGFR. To define how each of these single-nucleotide polymorphisms (SNPs) could affect renal function, we integrated GFR-associated loci with regulatory pathways, producing a molecular map of CKD. In kidney biopsy specimens from 157 European subjects representing nine different CKDs, renal transcript levels for 18 genes in proximity to the SNPs significantly correlated with GFR. These 18 genes were mapped into their biologic context by testing coregulated transcripts for enriched pathways. A network of 97 pathways linked by shared genes was constructed and characterized. Of these pathways, 56 pathways were reported previously to be associated with CKD; 41 pathways without prior association with CKD were ranked on the basis of the number of candidate genes connected to the respective pathways. All pathways aggregated into a network of two main clusters comprising inflammation- and metabolism-related pathways, with the NRF2-mediated oxidative stress response pathway serving as the hub between the two clusters. In all, 78 pathways and 95% of the connections among those pathways were verified in an independent North American biopsy cohort. Disease-specific analyses showed that most pathways are shared between sets of three diseases, with closest interconnection between lupus nephritis, IgA nephritis, and diabetic nephropathy. Taken together, the network integrates candidate genes from genome-wide association studies into their functional context, revealing interactions and defining established and novel biologic mechanisms of renal impairment in renal diseases.

Measures of dependence among variables, and measures of information content and shared information have become valuable tools of multi-variable data analysis. Information measures, like marginal entropies, mutual and multi-information, have a number of significant advantages over more standard statistical methods, like their reduced sensitivity to sampling limitations than statistical estimates of probability densities. There are also interesting applications of these measures to the theory of complexity and to statistical mechanics. Their mathematical properties and relationships are therefore of interest at several levels. Of the interesting relationships between common information measures, perhaps none are more intriguing and as elegant as the duality relationships based on Mobius inversions. These inversions are directly related to the lattices (posets) that describe these sets of variables and their multi-variable measures. In this paper we describe extensions of the duality previously noted by Bell to a range of measures, and show how the structure of the lattice determines fundamental relationships of these functions. Our major result is a set of interlinked duality relations among marginal entropies, interaction information, and conditional interaction information. The implications of these results include a flexible range of alternative formulations of information-based measures, and a new set of sum rules that arise from path-independent sums on the lattice. Our motivation is to advance the fundamental integration of this set of ideas and relations, and to show explicitly the ways in which all these measures are interrelated through lattice properties. These ideas can be useful in constructing theories of complexity, descriptions of large scale stochastic processes and systems, and in devising algorithms and approximations for computations in multi-variable data analysis.

Whole Body Vibration (WBV) is becoming increasingly popular for helping to maintain bone mass and strengthening muscle. Vibration regimens optimized for bone maintenance often operate at hypogravity levels (<1G) and regimens for muscle strengthening often employ hypergravity (>1G) vibrations. The effect of vibratory loads on tendon and ligament properties is unclear though excessive vibrations may be injurious. Our objective was to evaluate how tendon gene expression and the mechanical/histological properties of tendon and ligament were affected in response to WBV in the following groups: no vibration, low vibration (0.3G peak-to-peak), and high vibration (2G peak-to-peak). Rats were vibrated for 20min a day, 5 days a week, for 5 weeks. Upon sacrifice, the medial collateral ligament (MCL), patellar tendon (PT), and the Achilles Tendon (AT) were isolated with insertion sites intact. All tissues were tensile tested to determine structural and material properties or used for histology. Patellar tendon was also subjected to quantitative RT-PCR to evaluate expression of anabolic and catabolic genes. No differences in biomechanical data between the control and the low vibration groups were found. There was evidence of significant weakness in the MCL with high vibration, but no significant effect on the PT or AT. Histology of the MCL and PT showed a hypercellular tissue response and some fiber disorganization with high vibration. High vibration caused an increase in collagen expression and a trend for an increase in IGF-1 expression suggesting a potential anabolic response to prevent tendon overuse injury.

Genome-wide association studies have proven to be highly effective at defining relationships between single nucleotide polymorphisms (SNPs) and clinical phenotypes in complex diseases. Establishing a mechanistic link between a noncoding SNP and the clinical outcome is a significant hurdle in translating associations into biological insight. We demonstrate an approach to assess the functional context of a diabetic nephropathy (DN)-associated SNP located in the promoter region of the gene FRMD3 .T he approach integrates pathway analyses with transcriptional regulatory patternbased promoter modeling and allows the identification of a transcriptional framework affected by the DN-associated SNP in the FRMD3 promoter. This framework provides a testable hypothesis for mechanisms of genomic variation and transcriptional regulation in the context of DN. Our model proposes a possible transcriptional link through which the polymorphism in the FRMD3 promoter could influence transcriptional regulation within the bone morphogenetic protein (BMP)-signaling pathway. These findings provide the rationale to interrogate the biological link between FRMD3 and the BMP pathway and serve as an example of functional genomics-based hypothesis generation. Diabetes 62:2605–2612, 2013

OBJECTIVES:Evaluate the use of deferoxamine in a calcium sulfate carrier to promote fracture healing in a critical bone defect model. METHODS:43 female retired breeders were divided randomly into Control, Carrier, DFO and BMP groups and appropriate agents placed at the osteotomy site. RESULTS:There was a significant difference in the mean gap between groups Control vs DFO and Control vs BMP. A higher mean number of cortices were bridged in the DFO group as compared to the Control group. CONCLUSIONS:Our study demonstrated that DFO helped reduce the gap in this critical tibia defect.

Genome-wide association studies have proven to be highly effective at defining relationships between single nucleotide polymorphisms (SNPs) and clinical phenotypes in complex diseases. Establishing a mechanistic link between a noncoding SNP and the clinical outcome is a significant hurdle in translating associations into biological insight. We demonstrate an approach to assess the functional context of a diabetic nephropathy (DN)-associated SNP located in the promoter region of the gene FRMD3. The approach integrates pathway analyses with transcriptional regulatory pattern-based promoter modeling and allows the identification of a transcriptional framework affected by the DN-associated SNP in the FRMD3 promoter. This framework provides a testable hypothesis for mechanisms of genomic variation and transcriptional regulation in the context of DN. Our model proposes a possible transcriptional link through which the polymorphism in the FRMD3 promoter could influence transcriptional regulation within the bone morphogenetic protein (BMP)-signaling pathway. These findings provide the rationale to interrogate the biological link between FRMD3 and the BMP pathway and serve as an example of functional genomics-based hypothesis generation.

Diabetic kidney disease, or diabetic nephropathy (DN), is a major complication of diabetes and the leading cause of end-stage renal disease (ESRD) that requires dialysis treatment or kidney transplantation. In addition to the decrease in the quality of life, DN accounts for a large proportion of the excess mortality associated with type 1 diabetes (T1D). Whereas the degree of glycemia plays a pivotal role in DN, a subset of individuals with poorly controlled T1D do not develop DN. Furthermore, strong familial aggregation supports genetic susceptibility to DN. However, the genes and the molecular mechanisms behind the disease remain poorly understood, and current therapeutic strategies rarely result in reversal of DN. In the GEnetics of Nephropathy: an International Effort (GENIE) consortium, we have undertaken a meta-analysis of genomewide association studies (GWAS) of T1D DN comprising similar to 2.4 million single nucleotide polymorphisms (SNPs) imputed in 6,691 individuals. After additional genotyping of 41 top ranked SNPs representing 24 independent signals in 5,873 individuals, combined meta-analysis revealed association of two SNPs with ESRD: rs7583877 in the AFF3 gene (P = 1.2 x 10(-8)) and an intergenic SNP on chromosome 15q26 between the genes RGMA and MCTP2, rs12437854 (P = 2.0 x 10(-9)). Functional data suggest that AFF3 influences renal tubule fibrosis via the transforming growth factor-beta (TGF-beta 1) pathway. The strongest association with DN as a primary phenotype was seen for an intronic SNP in the ERBB4 gene (rs7588550, P = 2.1 x 10(-7)), a gene with type 2 diabetes DN differential expression and in the same intron as a variant with cis-eQTL expression of ERBB4. All these detected associations represent new signals in the pathogenesis of DN.

Previous work shows that gene associations and network properties common between pairs of diseases can provide molecular evidence of comorbidity, but relationships among diseases may extend to larger groups. Formal concept analysis allows the study of multiple diseases based on a concept lattice whose structure indicates gene set commonality. We use the concept lattice for gene associations to evaluate the complexity of the relationships among diseases, and to identify concepts whose gene sets are candidates for further functional analysis. For this, we define a heuristic on the lattice structure that allows the identification of concepts whose gene sets indicate strong relationships among the included diseases, which are distinguished from other diseases in the family. Applying this approach to a family of renal diseases we demonstrate that this approach finds gene sets that may be promising for studying common (and differing) mechanism among a family of comorbid or phenotypically related diseases.

A tight interplay of genetic predisposition and environmental factors define the onset and the rate of progression of chronic renal disease. We are seeing a rapid expansion of information about genetic loci associated with kidney function and complex renal disease. However, discovering the functional links that bridge the gap from genetic risk loci to disease phenotype is one of the main challenges ahead. Risk loci are currently assigned to a putative context using the functional annotation of the closest genes via a guilt-by-proximity approach. These approaches can be extended by strategies integrating genetic risk loci with kidney-specific, genome-wide gene expression. Risk loci-associated transcripts can be assigned a putative disease-specific function using gene expression coregulation networks. Ultimately, genotype-phenotype dependencies postulated from these associative approaches in humans need to be tested via genetic modification in model organisms. In this review, we survey strategies that employ human tissue-specific expression and the use of model organisms to identify and validate the functional relationship between genotype and phenotype in renal disease. Strategies to unravel how genetic risk and environmental factors orchestrate renal disease manifestation can be the first steps toward a more integrated, holistic approach urgently needed for chronic renal diseases. Kidney International (2012) 81, 14-21; doi:10.1038/ki.2011.359; published online 19 October 2011

Background: Bioinformatics visualization tools are often not robust enough to support biomedical specialists' complex exploratory analyses. Tools need to accommodate the workflows that scientists actually perform for specific translational research questions. To understand and model one of these workflows, we conducted a case-based, cognitive task analysis of a biomedical specialist's exploratory workflow for the question: What functional interactions among gene products of high throughput expression data suggest previously unknown mechanisms of a disease?Results: From our cognitive task analysis four complementary representations of the targeted workflow were developed. They include: usage scenarios, flow diagrams, a cognitive task taxonomy, and a mapping between cognitive tasks and user-centered visualization requirements. The representations capture the flows of cognitive tasks that led a biomedical specialist to inferences critical to hypothesizing. We created representations at levels of detail that could strategically guide visualization development, and we confirmed this by making a trial prototype based on user requirements for a small portion of the workflow.Conclusions: Our results imply that visualizations should make available to scientific users "bundles of features" consonant with the compositional cognitive tasks purposefully enacted at specific points in the workflow. We also highlight certain aspects of visualizations that: (a) need more built-in flexibility; (b) are critical for negotiating meaning; and (c) are necessary for essential metacognitive support.

The standardization and wider use of electronic medical records (EMR) creates opportunities for better understanding patterns of illness and care within and across medical systems. Our interest is in the temporal history of event codes embedded in patients' records, specifically investigating frequently occurring sequences of event codes across patients. In studying data from more than 1.6 million patient histories at the University of Michigan Health system we quickly realized that frequent sequences, while providing one level of data reduction, still constitute a serious analytical challenge as many involve alternate serializations of the same sets of codes. To further analyze these sequences, we designed an approach where a partial order is mined from frequent sequences of codes. We demonstrate an EMR mining system called EMRView that enables exploration of the precedence relationships to quickly identify and visualize partial order information encoded in key classes of patients. We demonstrate some important nuggets learned through our approach and also outline key challenges for future research based on our experiences.

Whole body vibration (WBV) has been extensively studied as an anabolic stimulus for bone and muscle. Therapeutic WBV delivers low magnitude, high frequency vibrations to tissues, eliciting biological and structural responses. This study investigated the effect of 0.3G (Peak-to-Peak), 30Hz sinusoidal vibration on intact flexor carpi ulnaris tendons in rats. Experimental rats were subjected to twenty minutes of WBV daily for five days a week for a total of five weeks. The tendon cross-sectional area and the structural properties of the muscle-tendon-bone unit under tensile loading to failure were evaluated. Initial body weights were similar between the groups and the mean change in body weight of the animals of each group did not differ. The cross-sectional area of the tendons of the vibrated animals was found to be 32% greater (P<0.05) than the controls and the structural stiffness of the vibrated tendons was found to be 41% greater (P<0.05) than the controls. For specimens that failed in the midsubstance of the tendon, a trend (P=0.087) for increased ultimate load was observed in the vibrated tendons compared to the controls. No differences in material properties were observed except for the strain to ultimate load, which was reduced 22% in the vibrated group. These initial findings suggest that vibration may serve as an anabolic stimulus to tendon similar to its effects on bone and muscle. These findings are important as they open the potential that low magnitude, high frequency vibration might serve as a means to accelerate tendon healing.