Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Fluid management and goal-directed therapy as an adjunct to Enhanced Recovery After Surgery (ERAS)

© 2014, Canadian Anesthesiologists' Society.Optimal perioperative fluid management is an important component of Enhanced Recovery After Surgery (ERAS) pathways. Fluid management within ERAS should be viewed as a continuum through the preoperative, intraoperative, and postoperative phases. Each phase is important for improving patient outcomes, and suboptimal care in one phase can undermine best practice within the rest of the ERAS pathway. The goal of preoperative fluid management is for the patient to arrive in the operating room in a hydrated and euvolemic state. To achieve this, prolonged fasting is not recommended, and routine mechanical bowel preparation should be avoided. Patients should be encouraged to ingest a clear carbohydrate drink two to three hours before surgery. The goals of intraoperative fluid management are to maintain central euvolemia and to avoid excess salt and water. To achieve this, patients undergoing surgery within an enhanced recovery protocol should have an individualized fluid management plan. As part of this plan, excess crystalloid should be avoided in all patients. For low-risk patients undergoing low-risk surgery, a “zero-balance” approach might be sufficient. In addition, for most patients undergoing major surgery, individualized goal-directed fluid therapy (GDFT) is recommended. Ultimately, however, the additional benefit of GDFT should be determined based on surgical and patient risk factors. Postoperatively, once fluid intake is established, intravenous fluid administration can be discontinued and restarted only if clinically indicated. In the absence of other concerns, detrimental postoperative fluid overload is not justified and “permissive oliguria” could be tolerated.

Reduced length of hospital stay in colorectal surgery after implementation of an enhanced recovery protocol.

BACKGROUND: Enhanced recovery after surgery (ERAS) is a multimodal approach to perioperative care that combines a range of interventions to enable early mobilization and feeding after surgery. We investigated the feasibility, clinical effectiveness, and cost savings of an ERAS program at a major U. S. teaching hospital. METHODS: Data were collected from consecutive patients undergoing open or laparoscopic colorectal surgery during 2 time periods, before and after implementation of an ERAS protocol. Data collected included patient demographics, operative, and perioperative surgical and anesthesia data, need for analgesics, complications, inpatient medical costs, and 30-day readmission rates. RESULTS: There were 99 patients in the traditional care group, and 142 in the ERAS group. The median length of stay (LOS) was 5 days in the ERAS group compared with 7 days in the traditional group (P < 0.001). The reduction in LOS was significant for both open procedures (median 6 vs 7 days, P = 0.01), and laparoscopic procedures (4 vs 6 days, P < 0.0001). ERAS patients had fewer urinary tract infections (13% vs 24%, P = 0.03). Readmission rates were lower in ERAS patients (9.8% vs 20.2%, P = 0.02). DISCUSSION: Implementation of an enhanced recovery protocol for colorectal surgery at a tertiary medical center was associated with a significantly reduced LOS and incidence of urinary tract infection. This is consistent with that of other studies in the literature and suggests that enhanced recovery programs could be implemented successfully and should be considered in U.S. hospitals.

Plantar Loading During Cutting While Wearing a Rigid Carbon Fiber Insert.

Context : Stress fractures are one of the most common injuries in sports, accounting for approximately 10% of all overuse injuries. Treatment of fifth metatarsal stress fractures involves both surgical and nonsurgical interventions. Fifth metatarsal stress fractures are difficult to treat because of the risks of delayed union, nonunion, and recurrent injuries. Most of these injuries occur during agility tasks, such as those performed in soccer, basketball, and lacrosse. Objective : To examine the effect of a rigid carbon graphite footplate on plantar loading during 2 agility tasks. Design :  Crossover study. Setting : Laboratory. Patients or Other Participants : A total of 19 recreational male athletes with no history of lower extremity injury in the past 6 months and no previous metatarsal stress fractures were tested. Main Outcome Measure(s) :  Seven 45° side-cut and crossover-cut tasks were completed in a shoe with or without a full-length rigid carbon plate. Testing order between the shoe conditions and the 2 cutting tasks was randomized. Plantar-loading data were recorded using instrumented insoles. Peak pressure, maximum force, force-time integral, and contact area beneath the total foot, the medial and lateral midfoot, and the medial, middle, and lateral forefoot were analyzed. A series of paired t tests was used to examine differences between the footwear conditions (carbon graphite footplate, shod) for both cutting tasks independently (α = .05). Results : During the side-cut task, the footplate increased total foot and lateral midfoot peak pressures while decreasing contact area and lateral midfoot force-time integral. During the crossover-cut task, the footplate increased total foot and lateral midfoot peak pressure and lateral forefoot force-time integral while decreasing total and lateral forefoot contact area. Conclusions : Although a rigid carbon graphite footplate altered some aspects of the plantar- pressure profile during cutting in uninjured participants, it was ineffective in reducing plantar loading beneath the fifth metatarsal.

Using ground reaction force to predict knee kinetic asymmetry following anterior cruciate ligament reconstruction.

Asymmetries in sagittal plane knee kinetics have been identified as a risk factor for anterior cruciate ligament (ACL) re-injury. Clinical tools are needed to identify the asymmetries. This study examined the relationships between knee kinetic asymmetries and ground reaction force (GRF) asymmetries during athletic tasks in adolescent patients following ACL reconstruction (ACL-R). Kinematic and GRF data were collected during a stop-jump task and a side-cutting task for 23 patients. Asymmetry indices between the surgical and non-surgical limbs were calculated for GRF and knee kinetic variables. For the stop-jump task, knee kinetics asymmetry indices were correlated with all GRF asymmetry indices (P < 0.05), except for loading rate. Vertical GRF impulse asymmetry index predicted peak knee moment, average knee moment, and knee work (R(2)  ≥ 0.78, P < 0.01) asymmetry indices. For the side-cutting tasks, knee kinetic asymmetry indices were correlated with the peak propulsion vertical GRF and vertical GRF impulse asymmetry indices (P < 0.05). Vertical GRF impulse asymmetry index predicted peak knee moment, average knee moment, and knee work (R(2)  ≥ 0.55, P < 0.01) asymmetry indices. The vertical GRF asymmetries may be a viable surrogate for knee kinetic asymmetries and therefore may assist in optimizing rehabilitation outcomes and minimizing re-injury rates.

Variation in the type and frequency of postoperative invasive Staphylococcus aureus infections according to type of surgical procedure.

OBJECTIVE: To determine the epidemiological characteristics of postoperative invasive Staphylococcus aureus infection following 4 types of major surgical procedures.design. Retrospective cohort study. SETTING: Eleven hospitals (9 community hospitals and 2 tertiary care hospitals) in North Carolina and Virginia. PATIENTS: Adults undergoing orthopedic, neurosurgical, cardiothoracic, and plastic surgical procedures. METHODS: We used previously validated, prospectively collected surgical surveillance data for surgical site infection and microbiological data for bloodstream infection. The study period was 2003 through 2006. We defined invasive S. aureus infection as either nonsuperficial incisional surgical site infection or bloodstream infection. Nonparametric bootstrapping was used to generate 95% confidence intervals (CIs). P values were generated using the Pearson chi2 test, Student t test, or Wilcoxon rank-sum test, as appropriate. RESULTS: In total, 81,267 patients underwent 96,455 procedures during the study period. The overall incidence of invasive S. aureus infection was 0.47 infections per 100 procedures (95% CI, 0.43-0.52); 227 (51%) of 446 infections were due to methicillin-resistant S.aureus. Invasive S. aureus infection was more common after cardiothoracic procedures (incidence, 0.79 infections per 100 procedures [95%CI, 0.62-0.97]) than after orthopedic procedures (0.37 infections per 100 procedures [95% CI, 0.32-0.42]), neurosurgical procedures (0.62 infections per 100 procedures [95% CI, 0.53-0.72]), or plastic surgical procedures (0.32 infections per 100 procedures [95% CI, 0.17-0.47]) (P < .001). Similarly, S. aureus bloodstream infection was most common after cardiothoracic procedures (incidence, 0.57 infections per 100 procedures [95% CI, 0.43-0.72]; P < .001, compared with other procedure types), comprising almost three-quarters of the invasive S. aureus infections after these procedures. The highest rate of surgical site infection was observed after neurosurgical procedures (incidence, 0.50 infections per 100 procedures [95% CI, 0.42-0.59]; P < .001, compared with other procedure types), comprising 80% of invasive S.aureus infections after these procedures. CONCLUSION: The frequency and type of postoperative invasive S. aureus infection varied significantly across procedure types. The highest risk procedures, such as cardiothoracic procedures, should be targeted for ongoing preventative interventions.