SNA--a toolbox for the stoichiometric analysis of metabolic networks

BACKGROUND: Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem. RESULTS: SNA is a interactive, high performance toolbox for analysing the possible steady state behaviour of metabolic networks by computing the generating and elementary vectors of their flux and conversions cones. It also supports analysing the steady states by linear programming. The toolbox is implemented mainly in Mathematica and returns numerically exact results. It is available under an open source license from: http://bioinformatics.org/project/?group_id=546. CONCLUSION: Thanks to its performance and modular design, SNA is demonstrably useful in analysing genome scale metabolic networks. Further, the integration into Mathematica provides a very flexible environment for the subsequent analysis and interpretation of the results.

Matched-pair analysis of endovascular versus open surgical repair of abdominal aortic aneurysms in young patients at low risk

PURPOSE: To compare clinical outcomes of endovascular and open aortic repair of abdominal aortic aneurysms (AAAs) in young patients at low risk. It was hypothesized that endovascular aneurysm repair (EVAR) compares favorably with open aneurysm repair (OAR) in these patients. MATERIALS AND METHODS: Twenty-five patients aged 65 years or younger with a low perioperative surgical risk profile underwent EVAR at a single institution between April 1994 and May 2007 (23 men; mean age, 62 years+/-2.8). A sex- and risk-matched control group of 25 consecutive patients aged 65 years or younger who underwent OAR was used as a control group (23 men; mean age, 59 years+/-3.9). Patient outcomes and complications were classified according to Society of Vascular Surgery/International Society for Cardiovascular Surgery reporting standards. RESULTS: Mean follow-up times were 7.1 years+/-3.2 after EVAR and 5.9 years+/-1.8 after OAR (P=.1020). Total complication rates were 20% after EVAR and 52% after OAR (P=.0378), and all complications were mild or moderate. Mean intensive care unit times were 0.2 days+/-0.4 after EVAR and 1.1 days+/-0.4 after OAR (P<.0001) and mean lengths of hospital stay were 2.3 days+/-1.0 after EVAR and 5.0 days+/-2.1 after OAR (P<.0001). Cumulative rates of long-term patient survival did not differ between EVAR and OAR (P=.144). No AAA-related deaths or aortoiliac ruptures occurred during follow-up for EVAR and OAR. In addition, no surgical conversions were necessary in EVAR recipients. Cumulative rates of freedom from secondary procedures were not significantly different between the EVAR and OAR groups (P=.418). Within a multivariable Cox proportional-hazards analysis adjusted for patient age, maximum AAA diameter, and cardiac risk score, all-cause mortality rates (odds ratio [OR], 0.125; 95% CI, 0.010-1.493; P=.100) and need for secondary procedures (OR, 5.014; 95% CI, 0.325-77.410; P=.537) were not different between EVAR and OAR. CONCLUSIONS: Results from this observational study indicate that EVAR offers a favorable alternative to OAR in young patients at low risk.

Outcome of transmetatarsal amputations in diabetics using antibiotic beads

BACKGROUND: Diabetic patients with transmetatarsal amputation (TMA) for chronic forefoot ulceration or necrosis are at high risk for postoperative skin breakdown and subsequent amputation. Locally applied antibiotics may reduce the revision rate and improve the outcome. MATERIAL AND METHODS: In a retrospective comparative study, 60 diabetic patients (65 feet) with forefoot ulceration or necrosis were treated with TMA by three surgeons in three hospitals. In the "beads group'' (46 patients, 49 feet) TMA was combined with local application of bioabsorbable, tobramycin impregnated calcium sulphate beads (OsteoSet-T beads, Wright Medical, Memphis, TN) as a single-stage procedure. The remaining 16 patients had transmetatarsal amputation without beads at the surgeon's discretion and acted as a control group. For all patients, time to healing, length of hospital stay, number of revisions for wound breakdown and conversions to a higher-level amputation were retrospectively reviewed. Of the 60 patients 17 had died and three were lost to followup, leaving 40 patients available for latest followup at 29 months. The Foot ; Ankle Outcome Score, Foot Function index, SF-36, and Comorbidity score were recorded. RESULTS: The revision rate for wound breakdown after TMA was 8.2% (4/49) in the beads group, and 25% (4/16) in the control group (p<0.05). At latest followup, 27% (13/49) in the beads group, and 25% (4/16) in the control group had to be converted to transtibial amputation. Patients in the beads group scored worse for activities of daily living in the FAOS and SF-36 (p < 0.05), and demonstrated more health problems in the Comorbidity scores (not significant), indicating sicker individuals in the beads group. CONCLUSION: Bioabsorbable calcium sulphate antibiotic beads may be a useful addition for TMA for patients with non-healing diabetic ulcerations of the forefoot. The single-stage procedure could have a significant impact on the management of diabetic forefoot ulcerations by preventing additional hospital stays, improving the patient's quality of life and minimizing cost.

Whole Proteome Analysis of the Protozoan Parasite Trypanosoma brucei using Stable Isotope Labeling by Amino Acids in Cell Culture and Mass Spectrometry

The single-celled protozoan Trypanosoma brucei spp. is the causative agent of human African trypanosomiasis and nagana in cattle. Quantitative proteomics for the first time allowed for the characterization of the proteome from several different life stages of the parasite (1-3). To achieve this, stable isotope labeling by amino acids in cell culture (SILAC; (4)) was adapted to T. brucei spp. cultures. T. brucei cells grown in standard media with dialyzed fetal calf serum containing heavy isotope-labeled amino acids (arginine and lysine) show efficient incorporation of the labeled amino acids into the whole cell proteome (8-12 divisions) and no detectable amino acid conversions. The method can be applied to both of the major life stages of the parasite and in combination with RNAi or gene knock-out approaches.

Measurement of chi_c1 and chi_c2 production with sqrts = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χc1 and χc2 charmonium states are measured in pp collisions at √s = 7TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χc states are reconstructed through the radiative decay χc → J/ψγ (with J/ψ → μ+μ−) where photons are reconstructed from γ → e+e− conversions. The production rate of the χc2 state relative to the χc1 state is measured for prompt and non-prompt χc as a function of J/ψ transverse momentum. The prompt χc cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χc decays. The fractions of χc1 and χc2 produced in b-hadron decays are also measured.

First Signs of Emerging Psychosis

The majority of first-episode psychoses are preceded by a prodromal phase that is several years on average, frequently leads to some decline in psychosocial functioning and offers the opportunity for early detection within the framework of an indicated prevention. To this, two approaches are currently mainly followed. The ultra-high-risk (UHR) criteria were explicitly developed to predict first-episode psychosis within 12 months, and indeed the majority of conversions in clinical UHR samples seem to occur within the first 12 months of initial assessment. Their main criterion, the attenuated psychotic symptoms criterion, captures symptoms that resemble positive symptoms of psychosis (i.e. delusions, hallucinations and formal thought disorders) with the exception that some level of insight is still maintained, and these frequently compromise functioning already. In contrast, the basic symptom criteria try to catch patients at increased risk of psychoses at the earliest possible time, i.e. ideally when only the first subtle disturbances in information processing have developed that are experienced with full insight and do not yet overload the person's coping abilities, and thus have not yet resulted in any functional decline. First results from prospective studies not only support this view, but indicate that the combination of both approaches might be a more favorable way to increase sensitivity and detect risk earlier, as well as to establish a change-sensitive risk stratification approach.