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Background: COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct and analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software.Results: Here, we describe COBRA for Python (COBRApy), a Python package that provides support for basic COBRA methods. COBRApy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. COBRApy does not require MATLAB to function; however, it includes an interface to the COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance, COBRApy includes parallel processing support for computationally intensive processes.Conclusion: COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. © 2013 Ebrahim et al.; licensee BioMed Central Ltd.

Introduction: Constriction band syndrome (CBS) is a congenital limb anomaly frequently associated with clubfoot. Clubfeet in CBS patients may be associated with peroneal nerve dysfunction in the involved lower extremity; however, the etiology of this neuromuscular dysfunction is not clear. We sought to characterize the distribution of constriction bands on lower extremities with clubfoot and determine if neuromuscular deficit (NMD), defined here as having absent ankle dorsiflexion, was associated with ipsilateral proximal bands. Our secondary aim was to compare the treatment and outcomes of clubfeet with NMD to those without NMD., Methods: We performed a retrospective review of all patients with CBS and clubfoot presenting to our facility between January 1, 1998 and December 31, 2018. Treatment with the Ponseti method, at least 1 year of follow-up at this facility, and a detailed physical exam describing lower extremity neuromuscular function and the presence and location of constriction bands were required for inclusion in the study cohort., Results: Twenty children with 26 clubfeet were included. Forty-six percent (12/26) of the clubfeet had NMD. Clubfeet with and without NMD had ipsilateral thigh or leg constriction bands at similar rates [42% (5/12) vs. 43% (6/14), P =0.106], and the majority (7/12) of clubfeet with NMD did not have an ipsilateral thigh or leg band. While children with an NMD clubfoot tended toward more casts, relapses, and surgical procedures, these differences did not reach statistical significance. The use of a daytime AFO beyond age four was higher in the NMD clubfeet [58% (7/12) vs. 14% (2/14), P =0.04]., Conclusion: Clubfeet with neuromuscular deficits may occur in the absence of proximal ipsilateral constriction bands, suggesting they may be caused by mechanisms other than direct damage from visible constriction bands to underlying nerves. They can also coexist with arthrogrypotic conditions. Clubfeet with an NMD tended toward more casts, relapses, and surgeries than those without NMD, but these differences did not reach statistical significance. These patients often elect long-term use of a daytime AFO., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Background: While tibia vara is a disorder of the proximal tibial physis, femoral deformity frequently contributes to the overall limb malalignment. Our purpose was to determine how femoral varus deformity in tibia vara responds to growth modulation, with/without lateral tension band plating (LTBP) to the femur., Methods: One-hundred twenty-seven limbs undergoing LTBP for tibia vara were reviewed. All had tibial LTBP and 35 limbs also had femoral LTBP for varus. Radiographs were measured for correction of the mechanical lateral distal femoral angle (mLDFA) and mechanical axis deviation (MAD). Preoperative-femoral varus was defined with an age-adjusted guide: mLDFA >95 degrees for 2 to below 4 years and mLDFA >90 degrees for 4 to 18 years. The 35 limbs having femoral LTBP were compared with 50 limbs with femoral varus and no femoral LTBP. In addition, 42 limbs that did not have preoperative-femoral varus were followed. Patients with early-onset (below 7 y) tibia vara were compared with those with late-onset (≥8 y). Outcome success was based on published age-adjusted mLDFA and MAD norms., Results: Following femoral LTBP, the mean mLDFA decreased from 98.0 to 87.1 degrees. All femurs had some improvement, with 28/35 femurs (80%) achieving complete correction. One limb, with late follow-up, overcorrected, requiring reverse (medial) femoral tension band plating.For the 50 limbs with femoral varus and only tibial LTBP, 16/22 limbs (73%) with early-onset and 11/28 limbs (39%) with late-onset completely corrected their femoral deformities. If the limb had preoperative-femoral varus, femoral LTBP statistically correlated with successful mLDFA correction and improvement of MAD, only in the late-onset group.Forty-two limbs, without preoperative-femoral varus, had no change in their mean mLDFA of 87 degrees. However, 4 femurs (10%) ended with posttreatment varus., Conclusions: Femoral LTBP is effective in correcting femoral varus deformity in the tibia vara. For femoral varus associated with late-onset tibia vara, femoral LTBP should be considered. Those that had femoral LTBP had statistically more successful femoral and overall limb varus correction. However, in early-onset tibia vara, with associated femoral varus, observation is warranted because 73% of femurs are corrected without femoral intervention. This study was underpowered to show additional improvement with femoral LTBP in the early-onset group. Even limbs with normal femoral alignment, should be observed closely for the development of femoral varus, during tibial LTBP treatment for tibia vara., Level of Evidence: Level III., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Angular deformity correction with tension band plating has not been as successful in early-onset tibia vara (EOTV) as it has been in other conditions. Our hypothesis is that perioperative factors can predict the success of lateral tibial tension band plating (LTTBP) in patients with EOTV., Methods: A retrospective review was performed at 7 centers evaluating radiographic outcomes of LTTBP in patients with EOTV (onset <7 y of age). Single-event tibial LTTBP outcome was assessed through medial proximal tibial angle (MPTA). The final limb alignment following comprehensive limb growth modulation (CLGM), which could include multiple procedures, was assessed by mechanical axis zone (MAZone), mechanical tibio-femoral angle (mTFA), and mechanical axis deviation (MAD). Preoperative age, weight, deformity severity, medial physeal slope, and Langenskiöld classification +/- modification were investigated as predictors of outcome. Success was defined as the correction or overcorrection to normal age-adjusted alignment. The minimum follow-up was 2 years except when deformity correction, skeletal maturity, or additional surgery occurred., Results: Fifty-two patients with 80 limbs underwent 115 tibial LTTBP procedures at a mean age of 5.3 y, including 78 primary, 21 implant revisions, and 15 reimplantations for recurrence. Tibial LTTBP resulted in a mean change of +8.6 o in MPTA and corrected 53% of tibias. CLGM resulted in MAD correction for 54% of limbs.Univariate analysis showed that success was best predicted by preoperative age, weight, MPTA, and MAD. Multivariate analysis identified that preoperative-MPTA/MAD and preoperative-weight<70 kg were predictive of MPTA and MAD correction, respectively. The probability of success tables are presented for reference., Conclusion: Successful correction of MPTA to age-adjusted norms following a single-event LTTBP occurred in 53% of tibias and was best predicted by preoperative-MPTA and preoperative body weight <70 kg. Comprehensive growth modulation corrected limbs in 54%. The probability of correction to age-adjusted MAD is best estimated by preoperative-MAZone 1 or 2 (MAD ≤40 mm). Limbs with preoperative-MAD>80 mm improved, but ultimately all failed to correct completely with CLGM. Osteotomy may need to be considered with these severe deformities. While modified Langenskiöld classification and medial physeal slope have been shown to predict the outcome of osteotomy, they were not predictive for LTTBP. Change in MPTA was common after physeal untethering., Level of Evidence: Level-III., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Growth modulation in late-onset tibia vara (LOTV) has been reported to yield variable results. We hypothesized that parameters of deformity severity, skeletal maturity, and body weight could predict the odds of a successful outcome., Methods: A retrospective review of tension band growth modulation for LOTV (onset ≥8 y) was performed at 7 centers. Tibial/overall limb deformity and hip/knee physeal maturity were assessed on preoperative anteroposterior standing lower-extremity digital radiographs. Tibial deformity change with first-time lateral tibial tension band plating (first LTTBP) was assessed by medial proximal tibia angle (MPTA). Effects of a growth modulation series (GMS) on overall limb alignment were assessed by mechanical tibiofemoral angle (mTFA) and included changes from implant removal, revision, reimplantation, subsequent growth, and femoral procedures during the study period. The successful outcome was defined as radiographic resolution of varus deformity or valgus overcorrection. Patient demographics, characteristics, maturity, deformity, and implant selections were assessed as outcome predictors using multiple logistic regression., Results: Fifty-four patients (76 limbs) had 84 LTTBP procedures and 29 femoral tension band procedures. For each 1-degree decrease in preoperative MPTA or 1-degree increase in preoperative mTFA the odds of their successful correction decreased by 26% in the first LTTBP and 6% by GMS, respectively, controlling for maturity. The change in odds of success for GMS assessed by mTFA was similar when controlling for weight. Closure of a proximal femoral physis decreased the odds of success for postoperative-MPTA by 91% with first LTTBP and for final-mTFA by 90% with GMS, controlling for preoperative deformity. Preoperative weight ≥100 kg decreased the odds of success for final-mTFA with GMS by 82%, controlling for preoperative mTFA. Age, sex, race/ethnicity, type of implant, and knee center peak value adjusted age (a method for bone age) were not predictive of outcome., Conclusions: Resolution of varus alignment in LOTV using first LTTBP and GMS, as quantified by MPTA and mTFA, respectively, is negatively impacted by deformity magnitude, hip physeal closure, and/or body weight ≥100 kg. The presented table, utilizing these variables, is helpful in the prediction of the outcome of the first LTTBP and GMS. Even if complete correction is not predicted, growth modulation may still be appropriate to reduce deformity in high-risk patients., Level of Evidence: Level III., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Despite early osteotomy, many patients with infantile tibia vara (ITV) have persistent or recurrent varus deformity and disordered growth at the medial proximal tibial physis. Our hypothesis was that lateral tibial tension band plating (LTTBP) could guide correction., Methods: A retrospective review at 6 centers of 15 patients (16 extremities) was performed of LTTBP for varus deformity following early osteotomy in ITV, diagnosed≤4years of age. Correction of deformity parameters on digital standing anteroposterior lower extremity radiographs determined outcome., Results: Twenty-two LTTBP procedures were performed at mean age of 7.5 years, including 4 revisions for implant failure and 2 reimplantations for recurrence. Single event LLTBP, improved the medial proximal tibial angle with a mean change of 13.4 degrees (0.39 degrees/month). Eleven limbs had preoperative mechanical lateral distal femoral angle (mLDFA)>90 degrees. While n degree femoral procedures were performed, at study end, 11 femurs had mechanical lateral distal femoral angle≤90°. Pretreatment, 13 extremities had mechanical axis zone (MAZone) III varus (81%) and 3 had MAZone II varus (19%). LTTBP's were able to initially correct 13 limbs to MAZone I or valgus but 4 limbs rebounded to MAZone II varus after implant removal. Final limb alignment, after all surgeries and rebound, included 9 in MAZone I, 5 in MAZone II varus and 2 in MAZone III varus. Average follow-up was 3.0 years at mean 10.7 years of age. Fifteen procedures resulted in improvement in MAZone and 7 had no change. On average, those that improved were younger (7.3 vs. 8.0 y), weighed less (45.5 kg with body mass index 26.5 kg/m 2 vs. 67.8 kg and body mass index 35.7 kg/m 2 ), had lower mechanical axis deviation (37.1 mm vs. 43.9 mm), lower medial physeal slope (61.7 vs. 68.7 degrees) and had a higher percentage of open triradiate phases (87 vs. 57%)., Conclusions: LTTBP for residual varus, after initial osteotomy in ITV, resulted in 81% of limbs initially achieving MAZone I or valgus with implant failure revisions and femoral remodeling. Rebound after implant removal reduced the corrected rate to 56%. Ninety-four percent avoided osteotomy during the study period., Level of Evidence: IV., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Tension band plate and screw implants (TBI) are frequently used for temporary hemiepiphyseodeses to manage angular deformity in growing children. The reported implant breakage rate, when TBI is used for deformities in patients with Blount disease, is much higher than when used in other diagnoses. Our hypothesis is that perioperative factors can identify risks for TBI breakage., Methods: A retrospective case-control study was performed of 246 TBI procedures in 113 patients with Blount disease at 8 tertiary pediatric orthopaedic centers from 2008 to 2018. Patient demographics, age at diagnosis, weight, body mass index (BMI), radiographic deformity severity measures, location, and types of implants were studied. The outcome of implant breakage was compared with these perioperative factors using univariate logistic regression with Bonferroni correction for multiplicity to significance tests., Results: There were 30 broken implants (12%), failing at mean 1.6 years following implantation. Most failures involved the metaphyseal screws. Increased BMI was associated with increased implant breakage. Increased varus deformity was directly associated with greater implant breakage and may be a more important factor in failure for those below 7 years compared with those 8 years or above at diagnosis. There was a 50% breakage rate for TBI with solid 3.5 mm screws in Blount disease with onset 8 years or above of age. No demographic or implant factors were found to be significant., Conclusions: Breakage of TBI was associated with increased BMI and varus deformity in patients with Blount disease. Larger studies are required to determine the relative contribution and limits of each parameter. Solid 3.5 mm screws should be used with caution in TBI for late-onset Blount disease., Level of Evidence: Level III., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Patient-Reported Outcomes Measurement Information System (PROMIS) is a well-validated tool used to measure health-related quality of life for children and adolescents with chronic medical conditions. The current study evaluates PROMIS scores in 3 domains for children with Ponseti-treated idiopathic clubfoot., Methods: This is a retrospective cohort study of 77 children, ages 5 to 16 years, treated by Ponseti protocol for idiopathic clubfoot. Three pediatric PROMIS domains (Mobility, Pain Interference, and Peer Relationships) were administered between April 2017 and June 2018. One-way analysis of variance with Bonferroni post hoc and independent sample t tests were performed to explore differences across PROMIS domain scores by sex, age, initial Dimeglio score, laterality, bracing duration, and whether the child underwent tibialis anterior transfer., Results: In the self-reported group (ages 8 to 16), mean T-scores for all 3 domains in both unilaterally and bilaterally affected groups were within the normal range, with respect to the general reference pediatric population. However, children with unilateral clubfoot had a significantly higher mean Mobility T-score (54.77) than children with bilateral clubfoot (47.81, P=0.005). Children with unilateral clubfoot also had significantly lower mean pain scores (39.16) than their bilateral counterparts (46.56, P=0.005). Children who had braced >36 months had a significantly higher mean Mobility T-score (53.68) than children who braced ≤36 months (46.28, P=0.004).In the proxy group (ages 5 to 7), mean T-scores for all 3 domains in both laterality groups were within the normal range, with respect to the reference population. Children who had braced >36 months had a significantly higher mean Mobility T-score (52.75 vs. 49.15, P=0.014) and lower Pain Interference score (43.04 vs. 49.15, P=0.020) than children who braced ≤36 months., Conclusions: Children treated by Ponseti protocol for idiopathic clubfoot yielded PROMIS scores for Mobility, Pain Interference, and Peer Relationships domains similar to the reference population. Bracing duration >36 months and unilaterality were associated with less mobility impairment than their counterparts. These findings may help guide parent recommendations., Level of Evidence: Level III.

The aim of this study was to describe the design and baseline characteristics of participants enrolled in the prospective randomized-controlled Clubfoot Foot Abduction Brace Length of Treatment Study (FAB24). Foot abduction bracing is currently the standard of care for preventing clubfoot relapse. Current recommendations include full-time bracing for the first 3 months and then 8-12 h a day for 4 years; however, the optimal length of bracing is not known. The FAB24 trial is a clinical randomized study to determine the effectiveness of 2- versus 4-year foot abduction bracing. Participant enrollment for FAB24 was conducted at eight sites in North America and included enrollment and randomization of 139 participants with isolated clubfoot. This clinical trial will generate evidence-based data that will inform and improve patient care.

Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi-level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration of primary omics data reveals regularities that tie cellular processes together in Escherichia coli: the number of protein molecules made per mRNA transcript and the number of ribosomes required per translated protein molecule. Second, we show that genome-scale models, based on genomic and bibliomic data, enable quantitative synchronization of disparate data types. Integrating omics data with models enabled the discovery of two novel regularities: condition invariant in vivo turnover rates of enzymes and the correlation of protein structural motifs and translational pausing. These regularities can be formally represented in a computable format allowing for coherent interpretation and prediction of fitness and selection that underlies cellular physiology.

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Membranes play a crucial role in cellular functions. Membranes provide a physical barrier, control the trafficking of substances entering and leaving the cell, and are a major determinant of cellular ultra-structure. In addition, components embedded within the membrane participate in cell signaling, energy transduction, and other critical cellular functions. All these processes must share the limited space in the membrane; thus it represents a notable constraint on cellular functions. Membrane- and location-based processes have not yet been reconstructed and explicitly integrated into genome-scale models., Results: The recent genome-scale model of metabolism and protein expression in Escherichia coli (called a ME-model) computes the complete composition of the proteome required to perform whole cell functions. Here we expand the ME-model to include (1) a reconstruction of protein translocation pathways, (2) assignment of all cellular proteins to one of four compartments (cytoplasm, inner membrane, periplasm, and outer membrane) and a translocation pathway, (3) experimentally determined translocase catalytic and porin diffusion rates, and (4) a novel membrane constraint that reflects cell morphology. Comparison of computations performed with this expanded ME-model, named iJL1678-ME, against available experimental data reveals that the model accurately describes translocation pathway expression and the functional proteome by compartmentalized mass., Conclusion: iJL1678-ME enables the computation of cellular phenotypes through an integrated computation of proteome composition, abundance, and activity in four cellular compartments (cytoplasm, periplasm, inner and outer membrane). Reconstruction and validation of the model has demonstrated that the iJL1678-ME is capable of capturing the functional content of membranes, cellular compartment-specific composition, and that it can be utilized to examine the effect of perturbing an expanded set of network components. iJL1678-ME takes a notable step towards the inclusion of cellular ultra-structure in genome-scale models.

Genome-scale models (GEMs) of metabolism were constructed for 55 fully sequenced Escherichia coli and Shigella strains. The GEMs enable a systems approach to characterizing the pan and core metabolic capabilities of the E. coli species. The majority of pan metabolic content was found to consist of alternate catabolic pathways for unique nutrient sources. The GEMs were then used to systematically analyze growth capabilities in more than 650 different growth-supporting environments. The results show that unique strain-specific metabolic capabilities correspond to pathotypes and environmental niches. Twelve of the GEMs were used to predict growth on six differentiating nutrients, and the predictions were found to agree with 80% of experimental outcomes. Additionally, GEMs were used to predict strain-specific auxotrophies. Twelve of the strains modeled were predicted to be auxotrophic for vitamins niacin (vitamin B3), thiamin (vitamin B1), or folate (vitamin B9). Six of the strains modeled have lost biosynthetic pathways for essential amino acids methionine, tryptophan, or leucine. Genome-scale analysis of multiple strains of a species can thus be used to define the metabolic essence of a microbial species and delineate growth differences that shed light on the adaptation process to a particular microenvironment.

Growth is a fundamental process of life. Growth requirements are well-characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale and capable of explaining the high-level behavior of the cell as a whole. Here, we construct an ME-Model for Escherichia coli--a genome-scale model that seamlessly integrates metabolic and gene product expression pathways. The model computes ~80% of the functional proteome (by mass), which is used by the cell to support growth under a given condition. Metabolism and gene expression are interdependent processes that affect and constrain each other. We formalize these constraints and apply the principle of growth optimization to enable the accurate prediction of multi-scale phenotypes, ranging from coarse-grained (growth rate, nutrient uptake, by-product secretion) to fine-grained (metabolic fluxes, gene expression levels). Our results unify many existing principles developed to describe bacterial growth.

The generation of genome-scale data is becoming more routine, yet the subsequent analysis of omics data remains a significant challenge. Here, an approach that integrates multiple omics datasets with bioinformatics tools was developed that produces a detailed annotation of several microbial genomic features. This methodology was used to characterize the genome of Thermotoga maritima--a phylogenetically deep-branching, hyperthermophilic bacterium. Experimental data were generated for whole-genome resequencing, transcription start site (TSS) determination, transcriptome profiling, and proteome profiling. These datasets, analyzed in combination with bioinformatics tools, served as a basis for the improvement of gene annotation, the elucidation of transcription units (TUs), the identification of putative non-coding RNAs (ncRNAs), and the determination of promoters and ribosome binding sites. This revealed many distinctive properties of the T. maritima genome organization relative to other bacteria. This genome has a high number of genes per TU (3.3), a paucity of putative ncRNAs (12), and few TUs with multiple TSSs (3.7%). Quantitative analysis of promoters and ribosome binding sites showed increased sequence conservation relative to other bacteria. The 5'UTRs follow an atypical bimodal length distribution comprised of "Short" 5'UTRs (11-17 nt) and "Common" 5'UTRs (26-32 nt). Transcriptional regulation is limited by a lack of intergenic space for the majority of TUs. Lastly, a high fraction of annotated genes are expressed independent of growth state and a linear correlation of mRNA/protein is observed (Pearson r = 0.63, p<2.2 × 10(-16) t-test). These distinctive properties are hypothesized to be a reflection of this organism's hyperthermophilic lifestyle and could yield novel insights into the evolutionary trajectory of microbial life on earth., Competing Interests: The authors have declared that no competing interests exist.

There has been growing interest in disrupting bacterial virulence mechanisms as a form of infectious disease control through the use of 'anti-infective' drugs. Pseudomonas aeruginosa is an opportunistic pathogen noted for its intrinsic antibiotic resistance that causes serious infections requiring new therapeutic options. In this study, an analysis of the P. aeruginosa PAO1 deduced proteome was performed to identify pathogen-associated proteins. A computational screening approach was then used to discover drug repurposing opportunities, i.e. identifying approved drugs that bind and potentially disrupt the pathogen-associated protein targets. The selective oestrogen receptor modulator raloxifene, a drug currently used in the prevention of osteoporosis and/or invasive breast cancer in post-menopausal women, was predicted from this screen to bind P. aeruginosa PhzB2. PhzB2 is involved in production of the blue pigment pyocyanin produced via the phenazine biosynthesis pathway. Pyocyanin is toxic to eukaryotic cells and has been shown to play a role in infection in a mouse model, making it an attractive target for anti-infective drug discovery. Raloxifene was found to strongly attenuate P. aeruginosa virulence in a Caenorhabditis elegans model of infection. Treatment of P. aeruginosa wild-type strains PAO1 and PA14 with raloxifene resulted in a dose-dependent reduction in pyocyanin production in vitro; pyocyanin production and virulence were also reduced for a phzB2 insertion mutant. These results suggest that raloxifene may be suitable for further development as a therapeutic for P. aeruginosa infection and that such already approved drugs may be computationally screened and potentially repurposed as novel anti-infective/anti-virulence agents., (Copyright © 2012 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.)

Enzymes are thought to have evolved highly specific catalytic activities from promiscuous ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we found that 37% of its enzymes act on a variety of substrates and catalyze 65% of the known metabolic reactions. However, it is not apparent why these generalist enzymes remain. Here, we show that there are marked differences between generalist enzymes and specialist enzymes, known to catalyze a single chemical reaction on one particular substrate in vivo. Specialist enzymes (i) are frequently essential, (ii) maintain higher metabolic flux, and (iii) require more regulation of enzyme activity to control metabolic flux in dynamic environments than do generalist enzymes. Furthermore, these properties are conserved in Archaea and Eukarya. Thus, the metabolic network context and environmental conditions influence enzyme evolution toward high specificity.

Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

Background: Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas., Results: Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain., Conclusions: Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.

The initial genome-scale reconstruction of the metabolic network of Escherichia coli K-12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced E. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications.

After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome-scale metabolic models (GEMs). However, it is not known whether the predicted pathway usage in FBA solutions is consistent with gene and protein expression in the wild-type and evolved strains. Here, we report that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data. Moreover, when E. coli adapts to growth rate selective pressure, the evolved strains upregulate genes within the optimal growth predictions, and downregulate genes outside of the optimal growth solutions. In addition, bottlenecks from dosage limitations of computationally predicted essential genes are overcome in the evolved strains. We also identify regulatory processes that may contribute to the development of the optimal growth phenotype in the evolved strains, such as the downregulation of known regulons and stringent response suppression. Thus, differential gene and protein expression from wild-type and adaptively evolved strains supports observed growth phenotype changes, and is consistent with GEM-computed optimal growth states.

Study Design: Retrospective review of radiographic data., Objectives: This study sought to define interobserver and intraobserver variability to further delineate reliable means by which radiographs of patients with neuromuscular scoliosis can be examined., Summary of Background Data: Previous studies analyzed the use of Cobb angles in the measurement of idiopathic and congenital scoliosis, but no study until now describes a critical analysis of measurement in evaluating neuromuscular scoliosis., Methods: Forty-eight patients with neuromuscular scoliosis radiographs were reviewed. These were evaluated for Cobb angle, end vertebrae selection, Ferguson angle, apex of the curve, C7 balance, pelvic obliquity, Risser sign, status of the triradiate cartilage, kyphosis Cobb angle, endplate selection for kyphosis, and kyphotic index. Interclass and intraclass variability was examined with statistical analysis., Results: Cobb angle had an intraobserver variability was 5.7 degrees and the interobserver variability was 14.8 degrees . The intraobserver and interobserver variability for Ferguson angle was 6.8 degrees and 20.6 degrees, respectively. The kyphotic Cobb angle intraobserver variability was found to be 17.4 degrees, and the interobserver variability was 24.01 degrees ., Conclusions: Neuromuscular scoliosis radiographs can be reliably analyzed with the use of Cobb angle. Other forms of analysis, such as Ferguson angle, are not as reliable. Pelvic obliquity should be measured from the horizontal, as other methods are not as reliable. Kyphosis is best evaluated with the use of the kyphotic Cobb angle. Finally, it is felt that a separate anteroposterior pelvis radiograph should be used to assess skeletal maturity, as scoliosis films often truncate the vital anatomy necessary to determine skeletal maturity.

The purpose of this study was to determine whether the Pediatric Outcomes Data Collection Instrument (PODCI) measures differences in function between children with brachial plexus birth palsy (BPBP) who are candidates for shoulder tendon surgery and age-matched controls. The PODCI was administered prospectively to 23 children with BPBP who were candidates for shoulder tendon surgery. Their results were compared with published PODCI data for control subjects, and factors associated with function within the BPBP cohort were determined. Children in the BPBP cohort had significantly lower PODCI scores in upper extremity function, sports, and global function than control subjects. Limited active shoulder external rotation was significantly associated with lower functional scores. The PODCI measures diminished upper extremity function in children with BPBP who are candidates for shoulder tendon surgery, thereby showing promise as a tool for measuring baseline function and postoperative functional gains for children with BPBP.

The Pediatric Outcomes Data Collection Instrument (PODCI) questionnaire was used to quantify functional abilities of a group of unilateral upper extremity deficiency (U-UED) patients and compare them with "normal" control children. Sixty-four consecutive patients with U-UED were assessed. Parents and adolescent (ages 11-21) patients responded. Underlying diagnosis, amputation level, and type of prosthesis were recorded. Scores were compared for congenital versus traumatic etiologies for patients with various amputation levels, and for patients using prostheses versus those not using prostheses. In both parent and patient responses, PODCI scores were significantly lower than "normal" for upper extremity function and sports. Scores were similar for congenital and acquired amputees. Responses from adolescent patients showed progressively decreasing scores for upper extremity, transfers, sports, and global function with progressively proximal amputation levels. Patients using prostheses with different terminal devices did not significantly differ. Parent responses for prosthesis wearers showed lower comfort/pain scores (ie, increased pain) than non-prosthesis wearers, but no significant differences in function, including upper extremity function.

The results of operative treatment of scoliosis in Down syndrome at one institution are reviewed. Seven patients with progressive scoliosis who had undergone arthrodesis of the thoracolumbar spine were identified. Clinical and radiographic results were noted, as were any complications. Mean patient follow up was 9 years (range 2-25). All patients eventually showed radiographic evidence of solid fusion with no curve progression. One patient had undergone a revision procedure for pseudoarthrosis and failure of Dwyer instrumentation. Other complications included a lateral subluxation under the fusion area, pneumonia, and one asymptomatic hook dislodgment. Progressive deformities of the thoracolumbar spine in Down syndrome patients can be treated with fusion and instrumentation with cessation of progression. As is the case for upper cervical fusion in these patients, the complication rate is notable.

Study Design and Objective: A mechanical skull model was used to compare axial loads to failure for three marketed and one experimental halo ring., Summary of Background Data: Open-back halo rings have become increasingly popular; however, to the authors' best knowledge the literature provides no comparison of the fixation strength of an open-back halo versus the traditional closed design., Methods: A model biomechanically similar to a human skull was used to compare the axial force necessary to distract each of four halo rings to failure. Three clinically used halo rings were compared: a closed titanium ring, an open titanium ring, and an open graphite ring. One additional open titanium halo ring was constructed with an angular profile; this ring was compared with the clinically used halos., Results: The mean force to failure for the closed titanium ring significantly exceeded that for the open rings (P < 0.005). No significant differences were noted among the open halo rings., Discussion: The data obtained by use of this biomechanical model show that the closed halo ring provides distraction strength greater than that of the open rings, suggesting a more rigid system with the closed device. Use of an angular halo did not improve fixation strength in the open ring device. These findings may support use of a closed halo ring in cervical spine traction and immobilization, if this greater strength is shown to be sufficiently clinically important to offset any disadvantages of a closed ring.

The compression force exerted by Gardner-Wells tongs was compared with the force necessary to penetrate the cranial inner table with a Gardner-Wells tong pin. Load cells measured the force exerted by the spring-loaded Gardner-Wells tong pin on fresh cadaveric skull samples. Increasing forces were exerted until penetration of the inner table occurred. At the manufacturer's recommended, 1 mm indicator stem protrusion an average of 30 pounds of compressive force was exerted by the spring-loaded pin. The average force necessary to penetrate the inner table with the cadaveric specimens with the tong pin was 162 pounds. The force necessary to penetrate the inner table of the skull well exceeds that exerted by properly applied tongs, suggesting that the risk of inner table penetration is low.

A cohort of 93 patients with developmental dysplasia of the hip (DDH) treated with a Pavlik harness were evaluated to determine predictors of treatment failure. Failure was defined as failure to achieve or maintain hip reduction in the Pavlik harness. Of 93 patients (137 hips), 17 (26 hips) failed Pavlik harness treatment. Univariate risk factors for failure included bilaterality, initial clinical exam, and initial ultrasound (US) percent coverage. Clinical exam and initial percent coverage were multivariate risk factors for failure. Among initially clinically dislocatable hips, a low initial US alpha angle correlated with an increased likelihood of failure. All (6/6) patients with an initially irreducible hip and an initial coverage of <20% by US eventually failed treatment. Gender, side of pathology, and age at diagnosis and initiation of treatment did not correlate with failure. Irreducibility by physical exam combined with US coverage of <20% identified a patient group that uniformly failed Pavlik harness treatment. These patients may be candidates for alternative bracing, traction, or closed or open reduction.

Summary of Background Data: Unstable cervical spine fractures and dislocations are often reduced by the application of axial traction using a halo or Gardner-Wells tongs. Failure of tong or halo attachment can cause substantial morbidity and usually occurs at the pin-bone interface. Institutions commonly clean and reuse tongs. The effect of tong wear on pullout strength and the strength of the halo used as a traction device have not been documented., Methods: A skull model biomechanically similar to human calvarium was used to compare the axial pullout strengths of four sets of new tongs, three sets of rarely used tongs, and one set of heavily used tongs, as well as a standard four-pin halo., Results: The pullout strength of tongs tightened to the manufacturer's recommended level appeared to decrease with increased use. Measurement of the pin force generated by each set of tongs and of the spring constant of each spring, as well as inspection of the tongs after testing, suggested that the decrease in pull-out strength may be partly attributable to spring and/or pin wear. The pullout strength of the halo or of the new or slightly used tongs but not the heavily used tongs exceeded the maximum weight used clinically in cervical spine traction., Conclusion: The data suggest that consideration be given to replacement or recalibration of heavily used tongs.

This study reports the effects of Simplex bone cement powder (BC) on the proliferation and production of bone resorbing factors in vitro by human adherent monocytes/macrophages. Adherent peripheral blood cells were isolated from seven healthy individuals and exposed to a dispersion of BC powder (1 mg/mL), phytohemagglutinin (PHA, 40 micrograms/mL), or medium alone at different periods of cell incubation (days 0-2, 0-7, 5-7, or 10-12). Cell proliferation was quantified by incorporation of 3H-thymidine uptake. Culture supernatants were evaluated for levels of interleukin 1-like activity (IL-1) by murine thymocyte proliferation assay, prostaglandin E2 (PGE2) by radioimmunoassay, lysosomal enzyme activity (N-acetyl-beta-D-glucosaminidase and beta-glucuronidase using fluorometry, and collagen and casein degrading activity using radioactive substrates. Human adherent peripheral blood cells showed a proliferative response to PHA that coincided with cell maturation; BC did not inhibit PHA-induced cell proliferation of either adherent or nonadherent blood cells, indicating the non-toxic nature of these particles at the concentrations tested. BC stimulated increased release of the lysosomal enzyme N-acetyl-beta-D-glucosaminidase; the levels of PGE2, IL-1, collagenase, and caseinase were unchanged.

Potential differences in flow rates between reversed and in situ saphenous vein bypass grafts were evaluated. One hundred ten greater saphenous vein segments containing isolated valves were examined with fiber-optic angioscopy during pulsatile and nonpulsatile flow. Valve competency was determined, and the degree of luminal obstruction caused by the valve during reversed flow was calculated with caliper measurements of the video image. Flow measurements were obtained before and after valvulotomy, in reversed and nonreversed vein orientations. Increased flow rates occurred during pulsatile irrigation only, after valvulotomy in vein segments with diameters less than 2.5 mm (p less than 0.001, Bonferroni t test). In these small-diameter vein segments, the flow rate in reversed valve-intact vein was 94.4 +/- 28.9 ml/min (mean +/- 1 standard deviation), the flow rate in reversed valve-disrupted vein was 136.4 +/- 36.5 ml/min, and the flow rate in nonreversed valve-disrupted vein was 137.8 +/- 31.3 ml/min. In 22 vein segments, luminal obstruction caused by the intact valve was measured angioscopically. A small valve orifice was found to be related to a large increase in flow rate after valvulotomy (p less than 0.02, least-squares regression). In addition, veins with diameters less than 2.5 mm have significantly smaller valve orifices compared with veins with diameters greater than 2.5 mm. These results present important clinical implications as the number of distal extremity reconstructions increases.

Buspirone is a novel anxiolytic compound that does not produce the sedation often associated with the use of benzodiazepines. The present study evaluated the effects of this anxiolytic on sleep in rats surgically prepared for long-term recordings. Buspirone, at a dose of 3 mg/kg i.p., produced a significant increase in total wake time (P less than 0.05) compared with drug-free controls. At a dose of 10 mg/kg i.p., rats displayed altered sleep patterns with the most significant effects observed in the first third of recording period. These animals displayed increased wakefulness (P less than 0.001), decreased non-REM sleep (P less than 0.001), and an obliteration of REM sleep (P less than 0.02). These data support the suggestion that the clinically useful anxiolytic buspirone, unlike the benzodiazepines, does not induce sleep.