scPerturb: harmonized single-cell perturbation data

Analysis across a growing number of single-cell perturbation datasets is hampered by poor data interoperability. To facilitate development and benchmarking of computational methods, we collect a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We apply uniform quality control pipelines and harmonize feature annotations. The resulting information resource, scPerturb, enables development and testing of computational methods, and facilitates comparison and integration across datasets. We describe energy statistics (E-statistics) for quantification of perturbation effects and significance testing, and demonstrate E-distance as a general distance measure between sets of single-cell expression profiles. We illustrate the application of E-statistics for quantifying similarity and efficacy of perturbations. The perturbation-response datasets and E-statistics computation software are publicly available at scperturb.org. This work provides an information resource for researchers working with single-cell perturbation data and recommendations for experimental design, including optimal cell counts and read depth.

RECOVER identifies synergistic drug combinations in vitro through sequential model optimization

For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state-of-the-art results in silico for the prediction of synergy scores. However, databases of drug combinations are biased toward synergistic agents and results do not generalize out of distribution. During 5 rounds of experimentation, we employ sequential model optimization with a deep learning model to select drug combinations increasingly enriched for synergism and active against a cancer cell line-evaluating only ∼5% of the total search space. Moreover, we find that learned drug embeddings (using structural information) begin to reflect biological mechanisms. In silico benchmarking suggests search queries are ∼5-10× enriched for highly synergistic drug combinations by using sequential rounds of evaluation when compared with random selection or ∼3× when using a pretrained model.

In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis

Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.

Identifiability and experimental design in perturbation studies

MOTIVATION

A common strategy to infer and quantify interactions between components of a biological system is to deduce them from the network's response to targeted perturbations. Such perturbation experiments are often challenging and costly. Therefore, optimizing the experimental design is essential to achieve a meaningful characterization of biological networks. However, it remains difficult to predict which combination of perturbations allows to infer specific interaction strengths in a given network topology. Yet, such a description of identifiability is necessary to select perturbations that maximize the number of inferable parameters.

RESULTS

We show analytically that the identifiability of network parameters can be determined by an intuitive maximum-flow problem. Furthermore, we used the theory of matroids to describe identifiability relationships between sets of parameters in order to build identifiable effective network models. Collectively, these results allowed to device strategies for an optimal design of the perturbation experiments. We benchmarked these strategies on a database of human pathways. Remarkably, full network identifiability was achieved, on average, with less than a third of the perturbations that are needed in a random experimental design. Moreover, we determined perturbation combinations that additionally decreased experimental effort compared to single-target perturbations. In summary, we provide a framework that allows to infer a maximal number of interaction strengths with a minimal number of perturbation experiments.

AVAILABILITY AND IMPLEMENTATION

IdentiFlow is available at github.com/GrossTor/IdentiFlow.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Robust network inference using response logic

Motivation

A major challenge in molecular and cellular biology is to map out the regulatory networks of cells. As regulatory interactions can typically not be directly observed experimentally, various computational methods have been proposed to disentangling direct and indirect effects. Most of these rely on assumptions that are rarely met or cannot be adapted to a given context.

Results

We present a network inference method that is based on a simple response logic with minimal presumptions. It requires that we can experimentally observe whether or not some of the system’s components respond to perturbations of some other components, and then identifies the directed networks that most accurately account for the observed propagation of the signal. To cope with the intractable number of possible networks, we developed a logic programming approach that can infer networks of hundreds of nodes, while being robust to noisy, heterogeneous or missing data. This allows to directly integrate prior network knowledge and additional constraints such as sparsity. We systematically benchmark our method on KEGG pathways, and show that it outperforms existing approaches in DREAM3 and DREAM4 challenges. Applied to a novel perturbation dataset on PI3K and MAPK pathways in isogenic models of a colon cancer cell line, it generates plausible network hypotheses that explain distinct sensitivities toward various targeted inhibitors due to different PI3K mutants.

Availability and implementation

A Python/Answer Set Programming implementation can be accessed at github.com/GrossTor/response-logic. Data and analysis scripts are available at github.com/GrossTor/response-logic-projects.

Supplementary information

Supplementary data are available at Bioinformatics online.

Modelling signalling networks from perturbation data

Motivation

Intracellular signalling is realized by complex signalling networks, which are almost impossible to understand without network models, especially if feedbacks are involved. Modular Response Analysis (MRA) is a convenient modelling method to study signalling networks in various contexts.

Results

We developed the software package STASNet (STeady-STate Analysis of Signalling Networks) that provides an augmented and extended version of MRA suited to model signalling networks from incomplete perturbation schemes and multi-perturbation data. Using data from the Dialogue on Reverse Engineering Assessment and Methods challenge, we show that predictions from STASNet models are among the top-performing methods. We applied the method to study the effect of SHP2, a protein that has been implicated in resistance to targeted therapy in colon cancer, using a novel dataset from the colon cancer cell line Widr and a SHP2-depleted derivative. We find that SHP2 is required for mitogen-activated protein kinase signalling, whereas AKT signalling only partially depends on SHP2.

Availability and implementation

An R-package is available at https://github.com/molsysbio/STASNet.

Supplementary information

Supplementary data are available at Bioinformatics online.

P6498Linkage analysis of transvalvular flow patterns, histopathology and target gene expression in aortic valve disease

Objectives

Recent studies have shown that shear stress can alter the integrity and gene expression of the aortic wall. We aim to analyze the link between jet dynamic, histological alterations, and gene expression patterns of the proximal aorta in patients with aortic valve disease.

Methods

We prospectively identified a total of 139 consecutive patients who were referred for aortic valve replacement (AVR) from January 2012 through December 2015. All patients underwent pre-operative MRI assessment to determine the maximal shear stress area of the proximal aorta. Depending of the aorta diameter we subdivided our study population in three subgroup (i.e., patients with a diameter ≤40mm, 41–49mm and ≥50mm). Based on the MRI results, two aortic wall tissue samples were collected during surgery. One sample were acquired from an area of low wall shear stress (WSS) and the second from the area of maximal WSS. The samples were graded in seven histopathologic features.

For RNA isolation the tissue was disrupted using a Tissue Lyser II (Qiagen). For the gene expression analysis of h18S, hCCL2, hCOL1A1, hVCAM1, and hELN reverse transcription of RNA was carried out using the High-capacity cDNA kit (life-technologies,USA). Therefore, 125 ng total RNA from tissue samples were reversely transcribed into cDNA.

Results

Regardless of the aortic valve functional lesion (i.e., stenosis or regurgitation), the maximal area of WSS was in the major curvature of the proximal aorta (73%, n=102). We observed that in both tissue samples just the orientation of vascular smooth muscle cell was strongly related to the diameter of the ascending aorta (p=0.004 vs. p=0.0032). In the whole study population any significant correlation was found between maximal cross-sectional aortic diameter and genes expression. However, in the subgroup analysis we identified that the tissue samples who were exposed to higher wall shear stress and presented a diameter ≥50mm, showed a statically significant gene over-expresion of COL1A1 (p=0.041) and ELN (p=0.01). In the tissue samples with a low WSS we also identified a significant over-expression of CCL2 (p=0.005) and COL1A1 (p=0.01).

Conclusions

Tissue samples from the slow WSS area with a proximal aortic diameter ≥50mm presented elevated levels of inflammatory response genes (i.e, CCL2). On the other hand, samples that were exposed to higher WSS demonstrated more relation to changes in the architecture of the connective fibres (i.e., elastin and collagen).

Acknowledgement/Funding

None

Abstract PD7-03: Cost-effectiveness analysis of intraoperative radiotherapy for ductal carcinoma in situ

Background

Whole breast radiation therapy (WBRT) following lumpectomy for ductal carcinoma in situ (DCIS) is standard of care, however, the risk of local recurrence with and without radiation ranges as low as 0.9% vs. 6.7% over 7 years. Intraoperative radiotherapy (IORT) is a potential alternative with advantages of decreased toxicity to adjacent organs, convenience, and improved quality of life. While prospective trials of IORT for DCIS are ongoing, the objective of this study was to estimate the cost-effectiveness of IORT vs. WBRT vs. no radiation for DCIS.

Methods

We developed a Markov model using TreeAge Pro 2016 to evaluate the cost-effectiveness of WBRT, IORT, and no radiation in patients with DCIS following lumpectomy. Health states included disease free, local recurrence (ipsilateral DCIS or invasive cancer), distant recurrence or death due to breast cancer, and death due to non-breast cancer causes. A 10-year time horizon and societal perspective were used. Model input parameters were derived from the literature. Costs reflected 2016 Medicare rates. The primary endpoint was incremental cost-effectiveness ratio (ICER), defined as the difference in cost, divided by the difference in quality-adjusted life years (QALYs) of two interventions. We performed analyses of subgroups defined according to DCIS risk (histologic grade, Oncotype Dx® DCIS recurrence score, low risk per RTOG 9804 criteria) and endocrine therapy use (none, tamoxifen, aromatase inhibitor). Sensitivity analyses explored uncertainty in the model.

Results

IORT was the most cost-effective strategy, with an increase of 0.18 QALYs at an incremental cost of $4,728, corresponding to an ICER of $26,943/QALY when compared with no radiation therapy. WBRT resulted in an increase in 0.18 QALYs at an incremental cost of $6859, corresponding to an ICER of $39,085/QALY. For both strategies, the ICERs did not exceed the willingness to pay (WTP) threshold of $100,000.

IORT remained the most cost-effective strategy across DCIS risk groups, but was more cost-effective in higher risk patients, as demonstrated by lower ICERs. In low risk DCIS defined by RTOG 9804 criteria, no radiation was most cost-effective. The ICERs for IORT and WBRT, $152,753 and $208,204/QALY, respectively, exceeded the WTP threshold. IORT remained cost-effective in the setting of endocrine therapy use.

Incremental Cost-Effectiveness Ratios (ICER) for each radiation strategy for the base case and scenario analyses ICER ($/QALY) No RTIORTWBRTBase Case Analysis 26,94339,085    Scenario Analysis by DCIS Risk GroupHistologic Grade   - Low 36,81152,219- High 25,64337,137    Oncotype Dx DCIS Score   - Low 92,892126,398- High 32,00345,690    Low Risk DCIS 152,753208,204    Scenario Analysis by Endocrine TherapyNo Tamoxifen 23,38734,373Tamoxifen 47,81166,616    Tamoxifen 31,96146,272Aromatase Inhibitor 41,31658,674

Conclusion

IORT was the most cost-effective radiation strategy for DCIS compared to WBRT and no radiation. This applied to all subgroups with the exception of low-risk DCIS defined by RTOG 9804 criteria for whom no radiation was the most cost-effective strategy. These findings provide support for ongoing studies examining the role of IORT for DCIS with high-risk features, as well as alternative treatment strategies for low-risk DCIS.

Citation Format: Onishi M, Connolly EP, Wright JD, Vasan S, Gross T, Tsai W-Y, Chen L, Neugut AI, Accordino MK, Kalinsky K, Crew KD, Hershman DL. Cost-effectiveness analysis of intraoperative radiotherapy for ductal carcinoma in situ [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD7-03.

3D RNA and Functional Interactions from Evolutionary Couplings

Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional interactions of these RNA gene sequences. We mine the evolutionary sequence record to derive precise information about the function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions-e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by increasing sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA.

The influence of dispersal on a predator-prey system with two habitats

Dispersal between different habitats influences the dynamics and stability of populations considerably. Furthermore, these effects depend on the local interactions of a population with other species. Here, we perform a general and comprehensive study of the simplest possible system that includes dispersal and local interactions, namely a 2-patch 2-species system. We evaluate the impact of dispersal on stability and on the occurrence of bifurcations, including pattern forming bifurcations that lead to spatial heterogeneity, in 19 different classes of models with the help of the generalized modelling approach. We find that dispersal often destabilizes equilibria, but it can stabilize them if it increases population losses. If dispersal is nonrandom, i.e. if emigration or immigration rates depend on population densities, the correlation of stability with dispersal rates is positive in part of the models. We also find that many systems show all four types of bifurcations and that antisynchronous oscillations occur mostly with nonrandom dispersal.

Modulational instability and resonant wave modes act on the metastability of oscillator chains

We describe the emergence and interactions of breather modes and resonant wave modes within a two-dimensional ringlike oscillator chain in a microcanonical situation. Our analytical results identify different dynamical regimes characterized by the potential dominance of either type of mode. The chain is initially placed in a metastable state, which it can leave by passing over the brim of the applied Mexican-hat-like potential. We elucidate the influence of the different wave modes on the mean-first passage time. A central finding is that also in this complex potential landscape a fast noise-free escape scenario solely relying on nonlinear cooperative effects is accomplishable even in a low-energy setting.

Allele characterization of genes required for rpg4-mediated wheat stem rust resistance identifies Rpg5 as the R gene

A highly virulent form of the wheat stem rust pathogen Puccinia graminis f. sp. tritici race TTKSK is virulent on both wheat and barley, presenting a major threat to world food security. The recessive and temperature-sensitive rpg4 gene is the only effective source of resistance identified in barley (Hordeum vulgare) against P. graminis f. sp. tritici race TTKSK. Efforts to position clone rpg4 localized resistance to a small interval on barley chromosome 5HL, tightly linked to the rye stem rust (P. graminis f. sp. secalis) resistance (R) gene Rpg5. High-resolution genetic analysis and post-transcriptional gene silencing of the genes at the rpg4/Rpg5 locus determined that three tightly linked genes (Rpg5, HvRga1, and HvAdf3) are required together for rpg4-mediated wheat stem rust resistance. Alleles of the three genes were analyzed from a diverse set of 14 domesticated barley lines (H. vulgare) and 8 wild barley accessions (H. vulgare subsp. spontaneum) to characterize diversity that may determine incompatibility (resistance). The analysis determined that HvAdf3 and HvRga1 code for predicted functional proteins that do not appear to contain polymorphisms determining the compatible (susceptible) interactions with the wheat stem rust pathogen and were expressed at the transcriptional level from both resistant and susceptible barley lines. The HvAdf3 alleles shared 100% amino acid identity among all 22 genotypes examined. The P. graminis f. sp. tritici race QCCJ-susceptible barley lines with HvRga1 alleles containing the limited amino acid substitutions unique to the susceptible varieties also contained predicted nonfunctional rpg5 alleles. Thus, susceptibility in these lines is likely due to the nonfunctional RPG5 proteins. The Rpg5 allele analysis determined that 9 of the 13 P. graminis f. sp. tritici race QCCJ-susceptible barley lines contain alleles that either code for predicted truncated proteins as the result of a single nucleotide substitution, resulting in a stop codon at amino acid 161, a single cytosine indel causing a frame shift, and a stop codon at amino acid 217, or an indel that deleted the entire STPK domain. The three P. graminis f. sp. tritici race QCCJ-susceptible lines (Swiss landraces Hv489, Hv492, and Hv611) and the wild barley accession WBDC160 contain rpg5 alleles predicted to encode full-length proteins containing a nonsynonomous nucleotide substitution that results in the amino acid substitution E1287A. This amino acid substitution present in the uncharacterized C-terminal domain is not found in any resistant line and may be important to elicit the resistance reaction. These data suggest that rpg4-mediated resistance against many wheat stem rust pathogen races, including P. graminis f. sp. tritici race TTKSK, rely on the Rpg5 R gene; thus, rpg4- and Rpg5-mediated resistance rely on a common R gene and should not be considered completely distinct. The data also determined that Rpg5 gene-specific molecular markers could be used to detect rpg4-mediated wheat stem rust resistance for marker-assisted selection.

Novel in situ cell for Raman diagnostics of lithium-ion batteries

A novel in situ cell for Raman diagnostics of working lithium-ion batteries is described. The design closely mimics that of standard battery testing cells and therefore allows to obtain Raman spectra under representative electrochemical conditions. Both cathode and anode materials can be studied. First results on the intercalation of a Li1-xCoO2 cathode material demonstrate the potential of the experimental approach for structural studies and underline the importance of studying lithium-ion batteries at work.

The rpg4-mediated resistance to wheat stem rust (Puccinia graminis) in barley (Hordeum vulgare) requires Rpg5, a second NBS-LRR gene, and an actin depolymerization factor

The rpg4 gene confers recessive resistance to several races of wheat stem rust (Puccinia graminis f. sp. tritici) and Rpg5 provides dominant resistance against isolates of the rye stem rust (P. graminis f. sp. secalis) in barley. The rpg4 and Rpg5 genes are tightly linked on chromosome 5H, and positional cloning using high-resolution populations clearly separated the genes, unambiguously identifying Rpg5; however, the identity of rpg4 remained unclear. High-resolution genotyping of critical recombinants at the rpg4/Rpg5 locus, designated here as rpg4-mediated resistance locus (RMRL) delimited two distinct yet tightly linked loci required for resistance, designated as RMRL1 and RMRL2. Utilizing virus-induced gene silencing, each gene at RMRL1, i.e., HvRga1 (a nucleotide-binding site leucine-rich repeat [NBS-LRR] domain gene), Rpg5 (an NBS-LRR-protein kinase domain gene), and HvAdf3 (an actin depolymerizing factor-like gene), was individually silenced followed by inoculation with P. graminis f. sp. tritici race QCCJ. Silencing each gene changed the reaction type from incompatible to compatible, indicating that all three genes are required for rpg4-mediated resistance. This stem rust resistance mechanism in barley follows the emerging theme of unrelated pairs of genetically linked NBS-LRR genes required for specific pathogen recognition and resistance. It also appears that actin cytoskeleton dynamics may play an important role in determining resistance against several races of stem rust in barley.

Management of blunt injuries to the spleen

Background

Non-operative management (NOM) of blunt splenic injuries is nowadays considered the standard treatment. The present study identified selection criteria for primary operative management (OM) and planned NOM.

Methods

All adult patients with blunt splenic injuries treated at Berne University Hospital, Switzerland, between 2000 and 2008 were reviewed.

Results

There were 206 patients (146 men) with a mean(s.d.) age of 38·2(19·1) years and an Injury Severity Score of 30·9(11·6). The American Association for the Surgery of Trauma classification of the splenic injury was grade 1 in 43 patients (20·9 per cent), grade 2 in 52 (25·2 per cent), grade 3 in 60 (29·1 per cent), grade 4 in 42 (20·4 per cent) and grade 5 in nine (4·4 per cent). Forty-seven patients (22·8 per cent) required immediate surgery. Transfusion of at least 5 units of red cells (odds ratio (OR) 13·72, 95 per cent confidence interval 5·08 to 37·01), Glasgow Coma Scale score below 11 (OR 9·88, 1·77 to 55·16) and age 55 years or more (OR 3·29, 1·07 to 10·08) were associated with primary OM. The rate of primary OM decreased from 33·3 to 11·9 per cent after the introduction of transcatheter arterial embolization in 2005. Overall, 159 patients (77·2 per cent) qualified for NOM, which was successful in 143 (89·9 per cent). The splenic salvage rate was 69·4 per cent. In multivariable analysis age at least 40 years was the only factor independently related to failure of NOM (OR 13·58, 2·76 to 66·71).

Conclusion

NOM of blunt splenic injuries has a low failure rate. Advanced age is independently associated with an increased failure rate.

Impact of a multifunctional image-guided therapy suite on emergency multiple trauma care

Background

The multifunctional image-guided therapy suite (MIGTS), a combined diagnostic and operating theatre, is currently the subject of considerable interest. This study investigated the effect of instituting a MIGTS on the emergency treatment of multiply injured patients.

Methods

This prospective controlled intervention study (MIGTS versus conventional treatment) included consecutive multiply injured trauma patients (Injury Severity Score of 16 or more) admitted between February 2003 and April 2005 to a university hospital. Main outcome measures were time to computed tomography (CT) and number of in-hospital transfers.

Results

A total of 168 patients were enrolled, 87 in the MIGTS and 81 in the control group. On average, CT was started at least 13 min sooner in the MIGTS group (P < 0·001), and these patients underwent fewer within-hospital transfers before arrival in the intensive care unit (median 2 versus 4 for controls; odds ratio −2·92, P < 0·001). Team members indicated increased satisfaction with the quality of the MIGTS procedure over the course of the study (P = 0·009). Thirty-day mortality rate (17 per cent for MIGTS versus 22 per cent for controls; P = 0·420) and long-term outcome did not differ between the two groups.

Conclusion

Implementation of a MIGTS in the emergency treatment of multiple trauma significantly accelerated the procedure and reduced the number of in-hospital transports. Registration number: NCT0072213 (http://www.clinicaltrials.gov).

Biomaterial effects in articular cartilage tissue engineering using polyglycolic acid, a novel marine origin biomaterial, IGF-I, and TGF-beta 1

Bovine articular chondrocytes were seeded on either polyglycolic acid (PGA) non-woven mesh scaffolds or a biomatrix from the species Porites lutea (POR). These constructs were cultured for 6 weeks in the presence of insulin-like growth factor (IGF)-I (10 ng/ml or 100 ng/ml) or transforming growth factor (TGF)-beta 1 (5 ng/ml or 30 ng/ml) to determine the in-vitro articular cartilage regeneration capacity of each. Histology, deoxyribonucleic acid content, collagen I and II (immunohistochemistry and enzyme-linked immunosorbent assay), and glycosaminoglycan (GAG) contents were measured at 0 weeks, 2 weeks, and 6 weeks to assess the characteristics of chondrogenesis. Both scaffolds supported the maintenance of the chondrocytic phenotype, as evidenced by the predominance of collagen II and the presence of rounded chondrocytes embedded in lacunae. Regardless of growth factor treatment, cells cultured on PGA scaffolds produced more collagen type II than those cultured on POR. Conversely, by 6 weeks, cells cultured on POR scaffolds produced more GAG than those cultured on PGA scaffolds, again regardless of the growth factor used. Across the two groups, 100 ng/ml of IGF-I had the greatest overall effect in GAG content. This work indicates that PGA and the POR scaffolds are both effective growth matrices for articular cartilage, with each scaffold exhibiting different yet desirable profiles of articular cartilage growth.

Stabilization due to predator interference: comparison of different analysis approaches

We study the influence of the particular form of the functional response in two-dimensional predator-prey models with respect to the stability of the nontrivial equilibrium. This equilibrium is stable between its appearance at a transcritical bifurcation and its destabilization at a Hopf bifurcation, giving rise to periodic behavior. Based on local bifurcation analysis, we introduce a classification of stabilizing effects. The classical Rosenzweig-MacArthur model can be classified as weakly stabilizing, undergoing the paradox of enrichment, while the well known Beddington-DeAngelis model can be classified as strongly stabilizing. Under certain conditions we obtain a complete stabilization, resulting in an avoidance of limit cycles. Both models, in their conventional formulation, are compared to a generalized, steady-state independent two-dimensional version of these models, based on a previously developed normalization method. We show explicitly how conventional and generalized models are related and how to interpret the results from the rather abstract stability analysis of generalized models.

[Quality management of interdisciplinary treatment of polytrauma. Possibilities and limits of retrospective routine data collection]

BACKGROUND

The purpose of this study was to evaluate the quality of interdisciplinary multiple trauma management using routinely taken data.

METHODS

A retrospective analysis of all multiple traumatized patients [Injury Severity Score (ISS)>15] in a university hospital (n=172; time period 01.01.1997-31.12.1999) was carried out concerning epidemiological and clinical variables and hospital outcome (p<0.05).

RESULTS

The overall mortality was 22% [n=38; expected Trauma Injury Severity Score (TRISS) mortality 29%]. Significant parameters for worse outcome in univariate analysis were age>74 years, hypotension, decreasing hemoglobin level and prothrombin time, decreased Glasgow Coma Scale and the number of erythrocyte or plasma concentrates received in the initial period of treatment. The comparison of our results with the data of the German Association for Trauma Surgery registry demonstrated comparable results with respect to management sequence and outcome.

CONCLUSIONS

In the quality management of multiple trauma patients retrospective analysis of routinely registered parameters can be a reliable and practical alternative to time-consuming prospective studies when based on prognostic relevant data. Such a procedure allows a preliminary critical comparison with other centers.

Lung-surfactant-meconium interaction: in vitro study in bulk and at the air-solution interface

Lung surfactants (LSs) form a monolayer at the lung's alveoli air-solution interface and play a crucial role in making normal breathing possible by reducing the surface tension. LS are affected by various agents that hamper their normal functioning. Tobacco smoke [Bringezu, F.; Pinkerton, K. E.; Zasadzinski, J. A. Langmuir 2003, 19, 2900-2907] and meconium, the first excrement of the newborn, are examples for such LS poison. In neonates, intrauterine aspiration of meconium is a known cause for morbidity and mortality. We studied in vitro the interactions between modified porcine LSs (Curosurf), used as LS replacement, and meconium, as well as between their artificial analogues, phospholipids mixture, and taurocholic acid (TA), respectively. The interactions were examined both in the bulk solution and at the air-water interface, representing the pre- and postnatal situations. It was found that the artificial analogues represent the natural system reliably and exhibit similar effects. TA, a principle component of bile, is an amphiphilic sterol compound in which the hydrophilic and hydrophobic moieties are presented at different faces of the sterol plane. Here we found that TA affects the structure of both monolayers at the interface and surfactant aggregates in solution. A likely poisoning mechanism is by stereoselective penetration of TA into the lamellar or monolayer structures, thus disrupting the contiguous structure of the intact monolayer or the bilayer vesicle structure.

[Interdisciplinary emergency room management of trauma patients from the standpoint of coworkers]

INTRODUCTION

The purpose of this study was to examine whether staff questionnaire evaluation is useful for quality control in the emergency room (ER) setting.

METHODS

Consecutive anonymous questionnaires (Likert scale 1-5) were filled out by the involved medical staff in all ER trauma cases in a university hospital from July 2002 to December 2003 (analysis of variance, P<0.05).

RESULTS

In 171 ER cases, 844 staff members responded. Main criticisms concerned time management or satisfaction with personal ER training (Likert <4). Consultants rated the quality of their training significantly higher than younger doctors, two thirds of consultants vs one third of residents having passed an Advanced Trauma and Life Support course (P<0.001). Depending on responders' professional specialties and whether the situation concerned multiple trauma (Injury Severity Score >15), a significant systematic difference resulted.

CONCLUSION

Our standardized staff questionnaire evaluation was revealed to be a discriminative instrument for quality management of trauma cases in the ER. To confirm these findings, correlation with clinical outcome data and further validation of the method are needed.

Multiple-trauma management

BACKGROUND AND OBJECTIVE

Staff attitude plays a pivotal role in quality management. The objective of the present study was to further define how interdisciplinary emergency hospital staff experience their daily work and the extent to which the professional speciality and training of an individual influences his/her assessment of multiple-trauma team performance.

METHODS

The clinical staff involved in multiple-trauma emergency management of a university hospital was asked to answer a confidential questionnaire. Factorial analysis was used to identify 8 major dimensions from a total of 53 items.

RESULTS

The questionnaire was returned by 128 team members. All professional groups were most dissatisfied with the dimensions 'education and training', 'work sequence between specialities' and 'communication between specialities'. Assessment of the quality of in-hospital emergency-trauma management differed significantly between professional specialities (ANOVA, F=5.2; P=0.028); surgeons gave the highest ratings for all but one dimension. Having taken an Advanced Trauma Life Support (ATLS) course influenced significantly the total rating of multiple-trauma treatments of anaesthetists and surgeons (F=5.5; P=0.024).

CONCLUSIONS

The perceptions of interdisciplinary trauma team members without the completion of an ATLS training course were that they did not communicate enough with each other and that there were differences between their expectations and reality. The differences and the communication deficits were overcome in team members who had passed an ATLS course.

Central Nervous System Tumors in Donors: Misdiagnosis Carries a High Morbidity and Mortality

INTRODUCTION

The cost of misdiagnosis of central nervous system (CNS) tumors in donors has not been previously described. The purpose of this study was to examine the Israel Penn International Transplant Tumor Registry experience with these donors.

METHODS

All cases where an error in diagnosis was made due to intracranial hemorrhage from undiagnosed CNS tumors and where CNS metastases were misdiagnosed as primary brain tumor were examined.

RESULTS

Forty-two organ recipients with misdiagnosed primary brain deaths from 29 donors were examined. After transplantation these donors were identified with: melanoma (23%), renal cell carcinoma (19%), choriocarcinoma (12%), sarcoma (10%), Kaposi's sarcoma (7%), and variable tumors (22%). The majority of patients were renal allograft recipients (84%) followed by liver (n = 4) and lung recipients (n = 1). The most commonly diagnostic error was with intracranial hemorrhage (ICH) (62%). A donor-related transmission rate of 74% (31/42) was identified among those patients with a misdiagnosed brain death. The majority of donor-transmitted cancers were identified in the recipient allograft (71%). Sixty-four percent of recipients suffered diffuse metastatic disease. Overall survival was poor, with a 5-year survival rate of 32% (10/31). Explantation was performed in 17 patients with confirmed donor-transmitted cancer, and in these patients a survival benefit was noted (10/17, 59%, vs 0/14, 0%; P < .01).

CONCLUSIONS

Error in the diagnosis of donor brain death due to CNS tumors has significant and often fatal consequences. Allograft explantation for kidney recipients or retransplantation for extrarenal recipients may provide a survival benefit. Potential donors with unclear etiologies for brain death, particularly ICH, should be considered for a limited brain autopsy after donation.

Displaced anterior column acetabular fracture: closed reduction and percutaneous CT-navigated fixation

The purpose of this study is to demonstrate the feasibility of computer-tomography-navigated closed reduction and percutaneous fixation (CRPF) in a patient with an externally rotated left acetabular fracture. After a follow-up of 18 months the patient was pain-free and had a normal range of motion in both hip joints. Radiologically, the fracture was fully consolidated, remodelled, and there were no signs of osteoarthritis. To our knowledge, CT-navigated CRPF of a rotated acetabular fracture has not been reported before. Further studies regarding the feasibility of the method are warranted.

Neue Stabilisierungsverfahren an der proximalen Tibia (LISS/LCP)

Bei instabilen proximalen Tibiafrakturen kommt es infolge ungenügender Abstützung nicht selten zu Sekundärdislokationen mit konsekutiver Gelenksinkongruenz und Achsenfehlstellung. Doppelplattenosteosynthesen erhöhen zwar die Stabilität, sind aber wenig biologisch und führen leicht zu Wundheilungsproblemen. Neue Stabilisierungsverfahren wie das LISS (Less Invasive Stabilization System) und die LCP (Locked Compression Plate) ermöglichen eine winkelstabile und minimal invasive Osteosynthese. Dadurch können die Stabilität verbessert und Wundheilungsprobleme vermindert werden. Somit werden einfache Frakturen weiterhin mit den herkömmlichen Implantaten versorgt, bicondyläre Frakturen mit metaphysärer Trümmerzone und/oder ausgedehntem Weichteilschaden werden aber zunehmend mit minimal invasiven winkelstabilen Osteosyntheseverfahren stabilisiert.

Delayed Union of a Sacral Fracture: Percutaneous Navigated Autologous Cancellous Bone Grafting and Screw Fixation

Delayed or non-union of a sacral fracture is a serious clinical condition that may include chronic pain, sitting discomfort, gait disturbances, neurological problems, and inability to work. It is also a difficult reconstruction problem. Late correction of the deformity is technically more demanding than the primary treatment of acute pelvic injuries. Open reduction, internal fixation (ORIF), excision of scar tissue, and bone grafting often in a multi-step approach are considered to be the treatment of choice in delayed unions of the pelvic ring. This procedure implies the risk of neurological and vascular injuries, infection, repeated failure of union, incomplete correction of the deformity, and incomplete pain relief as the most important complications. We report a new approach for minimally invasive treatment of a delayed union of the sacrum without vertical displacement. A patient who suffered a Malgaigne fracture (Tile C1.3) was initially treated with closed reduction and percutaneous screw fixation (CRPF) of the posterior pelvic ring under CT navigation and plating of the anterior pelvic ring. Three months after surgery he presented with increasing hip pain caused by a delayed union of the sacral fracture. The lesion was successfully treated percutaneously in a single step procedure using CT navigation for drilling of the delayed union, autologous bone grafting, and screw fixation.

Internal olefins to linear amines

The selective synthesis of linear amines from internal olefins or olefin mixtures was achieved through a catalytic one-pot reaction consisting of an initial olefin isomerization followed by hydroformylation and reductive amination. Key to the success is the use of specially designed phosphine ligands in the presence of rhodium catalysts. This reaction constitutes an economically attractive and environmentally favorable synthesis of linear aliphatic amines.

[Pain management in surgical wards. Quality and solutions for improvement in the early postoperative period]

INTRODUCTION

Following guidelines pain levels should not exceed a score of 3 on the visual analog scale (VAS 1-10). We were interested in the actual surgical pain management of the postoperative period and the potential influences of a nurse-controlled intravenous morphine administration (NCA) on its quality.

METHODS

Interventional study: interview of patients and nursing staff and examination of records concerning pain treatment following surgery.

RESULTS

The interviews were conducted with 110 patients before and 125 patients after the intervention program. Before the intervention, one-half of the patients noted that they were never asked about their pain intensity within the first 24 h after surgery. Only 42% of the records showed at least one VAS documentation. Every fourth individual experienced a pain intensity > 3 without having received a supplementary pain medication. Following the morphine intervention program, documentation of pain scores increased significantly (72%; p < 0.0001) and more patients were familiar with the VAS (64% vs 46%; p < 0.0004). Median maximum as well as actual pain at the time of the interview decreased by one point (VAS). The percentage of patients whose supplementary pain prescription was totally used showed a significant increase (p = 0.035). Following morphine administration, no single individual complained about an undue waiting time in comparison to 15% of patients previously. Even though the morphine intervention project caused more work for the nursing staff, 75% of the personnel were convinced that the procedure was worth this investment.

CONCLUSION

This data revealed a relevant deficiency of surgical pain management. Already basic instructions on pain management can significantly improve this treatment. Assigning additional authority to the nursing staff, such as a nurse-based intravenous opioid administration, can significantly raise the motivation of the personnel as well as the satisfaction of the patients involved.

The deubiquitinating enzyme Ubp21p of fission yeast stabilizes a mutant form of protein kinase Prp4p

The protein kinase Prp4p of Schizosaccharomyces pombe is involved in control of the formation of active spliceosomes, phosphorylating the spliceosomal component Prp1p. The kinase domain of Prp4p is closely related to cyclin-dependent kinases (CDKs) and mitogen-activated kinases (MAPKs). A mutational analysis of the highly conserved amino acid sequence ALKHP in subdomain XI of this kinase showed that structural features of this sequence are important for the function of the kinase. We identified ubp21 as a high-copy-number suppressor of a mutation in the ALKHP motif. Characterization of this gene revealed that it encodes a deubiquitinating enzyme belonging to the family of ubiquitin-specific processing proteases (Ubps). The results presented in this report are consistent with the notion that the deubiquitinating activity of Ubp21p may be involved in regulating the steady-state levels of proteins including Prp4p.

[Technology integration and process management. Concept and implementation of a new platform for simultaneous diagnosis and therapy of acutely ill and injured patients and for elective computer assisted surgery (CAS)]

Modern imaging and computer technology gain more and more importance in surgery. This is true for elective and emergency diagnosis and treatment. However integration of technology and optimization of process management is severely behind. A new diagnostic-therapeutic platform should balance this deficit. The platform is composed of a fully equipped operation room environment with integrated high end computer-tomography with navigation, a digital subtraction angiography and an OR- and imaging-table particularly developed for this set-up. The platform may be used for elective diagnosis, for diagnosis and therapy in polytraumatized patients in one and the same location (one stop shop) and for computer assisted surgery (CAS). Bringing the technology to the patient and not the patient to the technology can save time consuming and potentially dangerous transports and expensive personnel can be reduced. Navigation-technology and high quality intra-operative imaging expand the spectrum of minimally invasive surgery.