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Background: Intensive Care Resources are heavily utilized during the COVID-19 pandemic. However, risk stratification and prediction of SARS-CoV-2 patient clinical outcomes upon ICU admission remain inadequate. This study aimed to develop a machine learning model, based on retrospective & prospective clinical data, to stratify patient risk and predict ICU survival and outcomes. Methods: A Germany-wide electronic registry was established to pseudonymously collect admission, therapeutic and discharge information of SARS-CoV-2 ICU patients retrospectively and prospectively. Machine learning approaches were evaluated for the accuracy and interpretability of predictions. The Explainable Boosting Machine approach was selected as the most suitable method. Individual, non-linear shape functions for predictive parameters and parameter interactions are reported. Results: 1039 patients were included in the Explainable Boosting Machine model, 596 patients retrospectively collected, and 443 patients prospectively collected. The model for prediction of general ICU outcome was shown to be more reliable to predict “survival”. Age, inflammatory and thrombotic activity, and severity of ARDS at ICU admission were shown to be predictive of ICU survival. Patients’ age, pulmonary dysfunction and transfer from an external institution were predictors for ECMO therapy. The interaction of patient age with D-dimer levels on admission and creatinine levels with SOFA score without GCS were predictors for renal replacement therapy. Conclusions: Using Explainable Boosting Machine analysis, we confirmed and weighed previously reported and identified novel predictors for outcome in critically ill COVID-19 patients. Using this strategy, predictive modeling of COVID-19 ICU patient outcomes can be performed overcoming the limitations of linear regression models. Trial registration “ClinicalTrials” (clinicaltrials.gov) under NCT04455451.
This paper reports on Monte Carlo simulation results for future measurements of the moduli of time-like proton electromagnetic form factors, |GE | and |GM|, using the ¯pp → μ+μ− reaction at PANDA (FAIR). The electromagnetic form factors are fundamental quantities parameterizing the electric and magnetic structure of hadrons. This work estimates the statistical and total accuracy with which the form factors can be measured at PANDA, using an analysis of simulated data within the PandaRoot software framework. The most crucial background channel is ¯pp → π+π−,due to the very similar behavior of muons and pions in the detector. The suppression factors are evaluated for this and all other relevant background channels at different values of antiproton beam momentum. The signal/background separation is based on a multivariate analysis, using the Boosted Decision Trees method. An expected background subtraction is included in this study, based on realistic angular distribuations of the background contribution. Systematic uncertainties are considered and the relative total uncertainties of the form factor measurements are presented.
NeuLAND (New Large-Area Neutron Detector) is the next-generation neutron detector for the R3B (Reactions with Relativistic Radioactive Beams) experiment at FAIR (Facility for Antiproton and Ion Research). NeuLAND detects neutrons with energies from 100 to 1000 MeV, featuring a high detection efficiency, a high spatial and time resolution, and a large multi-neutron reconstruction efficiency. This is achieved by a highly granular design of organic scintillators: 3000 individual submodules with a size of 5 × 5 × 250 cm3 are arranged in 30 double planes with 100 submodules each, providing an active area of 250 × 250 cm2 and a total depth of 3 m. The spatial resolution due to the granularity together with a time resolution of 150 ps ensures high-resolution capabilities. In conjunction with calorimetric properties, a multi-neutron reconstruction efficiency of 50% to 70% for four-neutron events will be achieved, depending on both the emission scenario and the boundary conditions allowed for the reconstruction method. We present in this paper the final design of the detector as well as results from test measurements and simulations on which this design is based.
The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at sqrt{s}=7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L_int = 5.6nb-1. The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p_t>1.3 GeV/c and rapidity |y|<0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the Psi(2S) and Csi_c resonances, is sigma_prompt-J/psi(pt > 1.3 GeV/c, |y| < 0.9) = 8.3 +- 0.8(stat.) +- 1.1(syst.) + 1.5 - 1.4(syst. pol.) micro barn. The cross section for the production of b-hadrons decaying to J/psi with p_t>1.3 GeV/c and |y|<0.9 is sigma_{J/psi<-h_B} = 1.46 +- 0.38(stat.) + 0.26 -0.32(syst.) micro barn. The results are compared to QCD model predictions. The shape of the p_t and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b-bbar pair total cross section and dsigma/dy at mid-rapidity.
The Masquelet technique for the treatment of large bone defects is a two‐stage procedure based on an induced membrane. The size of a scaffold is reported to be a critical factor for bone healing response. We therefore aimed to investigate the influence of the granule size of a bone graft substitute on bone marrow derived mononuclear cells (BMC) supported bone healing in combination with the induced membrane. We compared three different sizes of Herafill® granules (Heraeus Medical GmbH, Wehrheim) with or without BMC in vivo in a rat femoral critical size defect. A 10 mm defect was made in 126 rats and a membrane induced by a PMMA‐spacer. After 3 weeks, the spacer was taken out and membrane filled with different granule sizes. After 8 weeks femurs were taken for radiological, biomechanical, histological, and immunohistochemical analysis. Further, whole blood of the rat was incubated with granules and expression of 29 peptide mediators was assessed. Smallest granules showed significantly improved bone healing compared to larger granules, which however did not lead to an increased biomechanical stability in the defect zone. Small granules lead to an increased accumulation of macrophages in situ which could be assigned to the inflammatory subtype M1 by majority. Increased release of chemotactic respectively proangiogenic active factors in vitro compared to syngenic bone and beta‐TCP was observed. Granule size of the bone graft substitute Herafill® has significant impact on bone healing of a critical size defect in combination with Masquelet's technique in terms of bone formation and inflammatory.
The pT-differential inclusive production cross section of the prompt charm-strange meson Ds+ in the rapidity range |y|<0.5 was measured in proton–proton collisions at s=7 TeV at the LHC using the ALICE detector. The analysis was performed on a data sample of 2.98×108 events collected with a minimum-bias trigger. The corresponding integrated luminosity is Lint=4.8 nb−1. Reconstructing the decay Ds+→ϕπ+, with ϕ→K−K+, and its charge conjugate, about 480 Ds± mesons were counted, after selection cuts, in the transverse momentum range 2<pT<12 GeV/c. The results are compared with predictions from models based on perturbative QCD. The ratios of the cross sections of four D meson species (namely D0, D+, D⁎+ and Ds+) were determined both as a function of pT and integrated over pT after extrapolating to full pT range, together with the strangeness suppression factor in charm fragmentation. The obtained values are found to be compatible within uncertainties with those measured by other experiments in e+e−, ep and pp interactions at various centre-of-mass energies.
Identical neutral kaon pair correlations are measured in √s=7 TeV pp collisions in the ALICE experiment. One-dimensional Ks0Ks0 correlation functions in terms of the invariant momentum difference of kaon pairs are formed in two multiplicity and two transverse momentum ranges. The femtoscopic parameters for the radius and correlation strength of the kaon source are extracted. The fit includes quantum statistics and final-state interactions of the a0/f0 resonance. Ks0Ks0 correlations show an increase in radius for increasing multiplicity and a slight decrease in radius for increasing transverse mass, mT, as seen in ππ correlations in pp collisions and in heavy-ion collisions. Transverse mass scaling is observed between the Ks0Ks0 and ππ radii. Also, the first observation is made of the decay of the f2′(1525) meson into the Ks0Ks0 channel in pp collisions.
The elliptic, v2, triangular, v3, and quadrangular, v4, azimuthal anisotropic flow coefficients are measured for unidentified charged particles, pions, and (anti-)protons in Pb–Pb collisions at √sNN=2.76 TeV with the ALICE detector at the Large Hadron Collider. Results obtained with the event plane and four-particle cumulant methods are reported for the pseudo-rapidity range |η|<0.8 at different collision centralities and as a function of transverse momentum, pT, out to pT=20 GeV/c. The observed non-zero elliptic and triangular flow depends only weakly on transverse momentum for pT>8 GeV/c. The small pT dependence of the difference between elliptic flow results obtained from the event plane and four-particle cumulant methods suggests a common origin of flow fluctuations up to pT=8 GeV/c. The magnitude of the (anti-)proton elliptic and triangular flow is larger than that of pions out to at least pT=8 GeV/c indicating that the particle type dependence persists out to high pT.
The production cross section of electrons from semileptonic decays of beauty hadrons was measured at mid-rapidity (|y|<0.8) in the transverse momentum range 1<pT<8 GeV/c with the ALICE experiment at the CERN LHC in pp collisions at a center of mass energy √s=7 TeV using an integrated luminosity of 2.2 nb−1. Electrons from beauty hadron decays were selected based on the displacement of the decay vertex from the collision vertex. A perturbative QCD calculation agrees with the measurement within uncertainties. The data were extrapolated to the full phase space to determine the total cross section for the production of beauty quark–antiquark pairs.
The inclusive transverse momentum (pT) distributions of primary charged particles are measured in the pseudo-rapidity range |η|<0.8 as a function of event centrality in Pb–Pb collisions at √sNN=2.76 TeV with ALICE at the LHC. The data are presented in the pT range 0.15<pT<50 GeV/c for nine centrality intervals from 70–80% to 0–5%. The results in Pb–Pb are presented in terms of the nuclear modification factor RAA using a pp reference spectrum measured at the same collision energy. We observe that the suppression of high-pT particles strongly depends on event centrality. The yield is most suppressed in central collisions (0–5%) with RAA≈0.13 at pT=6–7 GeV/c. Above pT=7 GeV/c, there is a significant rise in the nuclear modification factor, which reaches RAA≈0.4 for pT>30 GeV/c. In peripheral collisions (70–80%), only moderate suppression (RAA=0.6–0.7) and a weak pT dependence is observed. The measured nuclear modification factors are compared to other measurements and model calculations.
The ALICE Collaboration has made the first measurement at the LHC of J/ψ photoproduction in ultra-peripheral Pb–Pb collisions at sNN=2.76 TeV. The J/ψ is identified via its dimuon decay in the forward rapidity region with the muon spectrometer for events where the hadronic activity is required to be minimal. The analysis is based on an event sample corresponding to an integrated luminosity of about 55 μb−1. The cross section for coherent J/ψ production in the rapidity interval −3.6<y<−2.6 is measured to be dσJ/ψcoh/dy=1.00±0.18(stat)−0.26+0.24(syst) mb. The result is compared to theoretical models for coherent J/ψ production and found to be in good agreement with those models which include nuclear gluon shadowing.
Purpose: The Masquelet technique for the treatment of large bone defects is a two-stage procedure based on an induced membrane. Compared to mature periosteum, the induced membrane differs significantly. However, both play a crucial role in bone regeneration. As part of a histological and radiological post-evaluation of an earlier project, we analyzed the influence of the granule size of the bone void filler Herafill® on development of periosteum regrowth in a critical size defect.
Methods: We compared three different sizes of Herafill® granules (Heraeus Medical GmbH, Wehrheim) in vivo in a rat femoral critical size defect (10 mm) treated with the induced membrane technique. After 8 weeks healing time, femurs were harvested and taken for histological and radiological analysis.
Results: A significantly increased regrowth of periosteum into the defect was found when small granules were used. Large granules showed significantly increased occurrence of bone capping. Small granules lead to significant increase in callus formation in the vicinity to the membrane.
Conclusion: The size of Herafill® granules has significant impact on the development of periosteal-like structures around the defect using Masquelet’s induced membrane technique. Small granules show significantly increased regrowth of periosteum and improved bone formation adjacent to the induced membrane.
Measurement of charm production at central rapidity in proton-proton collisions at √s = 2.76 TeV
(2012)
The pT-differential production cross sections of the prompt (B feed-down subtracted) charmed mesons D0, D+, and D∗+ in the rapidity range |y|<0.5, and for transverse momentum 1<pT<12 GeV/c, were measured in proton-proton collisions at s√=2.76 TeV with the ALICE detector at the Large Hadron Collider. The analysis exploited the hadronic decays D0→Kπ, D+→Kππ, D∗+→D0π, and their charge conjugates, and was performed on a Lint=1.1 nb−1 event sample collected in 2011 with a minimum-bias trigger. The total charm production cross section at s√=2.76 TeV and at 7 TeV was evaluated by extrapolating to the full phase space the pT-differential production cross sections at s√=2.76 TeV and our previous measurements at s√=7 TeV. The results were compared to existing measurements and to perturbative-QCD calculations. The fraction of cdbar D mesons produced in a vector state was also determined.
The first measurement of neutron emission in electromagnetic dissociation of 208Pb nuclei at the LHC is presented. The measurement is performed using the neutron Zero Degree Calorimeters of the ALICE experiment, which detect neutral particles close to beam rapidity. The measured cross sections of single and mutual electromagnetic dissociation of Pb nuclei at sNN−−−√ = 2.76 TeV with neutron emission are σsingle EMD=187.4±0.2 (stat.) +13.2−11.2 (syst.) b and σmutual EMD=5.7±0.1 (stat.) ±0.4 (syst.) b, respectively. The experimental results are compared to the predictions from a relativistic electromagnetic dissociation model.
Measurement of electrons from semileptonic heavy-flavor hadron decays in pp collisions at √s = 7 TeV
(2012)
The differential production cross section of electrons from semileptonic heavy-flavour hadron decays has been measured at mid-rapidity (|y|<0.5) in proton-proton collisions at s√=7 TeV with ALICE at the LHC. Electrons were measured in the transverse momentum range 0.5 <pT< 8 GeV/c. Predictions from a fixed order perturbative QCD calculation with next-to-leading-log resummation agree with the data within the theoretical and experimental uncertainties.
Background Bacterial DNA containing motifs of unmethylated CpG dinucleotides (CpG-ODN) initiate an innate immune response mediated by the pattern recognition receptor Toll-like receptor 9 (TLR9). This leads in particular to the expression of proinflammatory mediators such as tumor necrosis factor (TNF-alpha) and interleukin-1beta (IL-1beta). TLR9 is expressed in human and murine pulmonary tissue and induction of proinflammatory mediators has been linked to the development of acute lung injury. Therefore, the hypothesis was tested whether CpG-ODN administration induces an inflammatory response in the lung via TLR9 in vivo. Methods Wild-type (WT) and TLR9-deficient (TLR9-D) mice received CpG-ODN intraperitoneally (1668-Thioat, 1 nmol/g BW) and were observed for up to 6 hrs. Lung tissue and plasma samples were taken and various inflammatory markers were measured. Results In WT mice, CpG-ODN induced a strong activation of pulmonary NFKB as well as a significant increase in pulmonary TNF-alpha and IL-1beta mRNA/protein. In addition, cytokine serum levels were significantly elevated in WT mice. Increased pulmonary content of lung myeloperoxidase (MPO) was documented in WT mice following application of CpG-ODN. Bronchoalveolar lavage (BAL) revealed that CpG-ODN stimulation significantly increased total cell number as well as neutrophil count in WT animals. In contrast, the CpG-ODN-induced inflammatory response was abolished in TLR9-D mice. Conclusion This study suggests that bacterial CpG-ODN causes lung inflammation via TLR9.
Mesenchymal stromal/stem cells and their derivates are the most promising cell source for cell therapies in regenerative medicine. The application of extracellular vesicles (EVs) as cell-free therapeuticals requires particles with a maximum regenerative capability to enhance tissue and organ regeneration. The cargo of mRNA and microRNA (miR) in EVs after hypoxic preconditioning has not been extensively investigated. Therefore, the aim of our study was the characterization of mRNA and the miR loading of EVs. We further investigated the effects of the isolated EVs on renal tubular epithelial cells in vitro. We found 3131 transcripts to be significantly regulated upon hypoxia. Only 15 of these were downregulated, but 3116 were up-regulated. In addition, we found 190 small RNAs, 169 of these were miRs and 21 were piwi-interacting RNAs (piR). However, only 18 of the small RNAs were significantly altered, seven were miRs and 11 were piRs. Interestingly, all seven miRs were down-regulated after hypoxic pretreatment, whereas all 11 piRs were up-regulated. Gene ontology term enrichment and miR-target enrichment analysis of the mRNAs and miR were also performed in order to study the biological background. Finally, the therapeutic effect of EVs on human renal tubular epithelial cells was shown by the increased expression of three anti-inflammatory molecules after incubation with EVs from hypoxic pretreatment. In summary, our study demonstrates the altered mRNA and miR load in EVs after hypoxic preconditioning, and their anti-inflammatory effect on epithelial cells.
Der menschliche Knochen besitzt, als Folge einer Verletzung oder eines chirurgischen Eingriffs, eine große Fähigkeit zur Reparatur und Regeneration. Die Knochenheilung beinhaltet ein komplexes Zusammenspiel von Zellen, Wachstumsfaktoren, Zytokinen sowie der extrazellulären Matrix (Hoerth et al. 2014). Nichtsdestotrotz führt ein Knochenbruch zu einer dramatischen Veränderung der mechanischen Belastbarkeit an der Verletzungsstelle. Der Abstand zwischen den beiden Frakturenden bildet einen entscheidenden Faktor in der Knochenheilung. Hier wird zwischen der primären, der osteonalen Knochenheilung und der sekundären, der kallusformierenden Knochenheilung unterschieden. Umso größer der Frakturspalt ist, desto größer wird die Instabilität, die Heilungsverzögerung und damit auch die Gefahr einer Pseudoarthrose (Hoerth et al., 2014; Marsell et Einhorn, 2011).
Große diaphysale Defekte werden meistens durch Traumata, Infektionen oder Tumore bedingt. Sie werden als critical size defects (CSD) bezeichnet, wenn eine chirurgische Intervention zur Heilung notwendig ist (Rosset et al., 2014). Langstreckige Knochendefekte stellen immer noch eine sehr große Herausforderung in der rekonstruktiven Chirurgie dar. Deswegen ist die Untersuchung und Weiterentwicklung von implantierbaren biomedizinischen Materialien bei der Behandlung von CSD eine wichtige Aufgabe.
Im Augenblick ist die häufigste Behandlungsmethode großer diaphysaler Defekte die Autologe Spongiosaplastik (ASP) und wird als Goldstandart der Therapie bezeichnet. Jedoch stehen die autologen Knochenmaterialien nur begrenzt zur Verfügung und verursachen viele Entnahmemorbiditäten. Darüber hinaus gibt es allogene, xenogene und synthetische Knochentransplantate. Dennoch ist noch keine der Therapiemöglichkeiten so ausgereift, dass die ASP dadurch ersetzt werden könnte. Die allogenen und xenogenen Materialien sind von der Menge unbegrenzt, besitzen aber eine niedrigere Biokompatibilität, höhere Infektionsgefahr und schlechtere Ergebnisse in der Langzeitwirkung (Wang et al., 2014).
Ein weiterer Nachteil gegenüber der ASP besteht darin, dass die synthetischen Knochenersatzmaterialien keine osteoinduktiven und osteogenen Eingenschaften besitzen. Eine Möglichkeit diese Qualitäten zu erhalten ist, sie mit Zellsuspensionen, wie z.B. bone marrow mononuclear cells (BMC), zu kombinieren und somit zu versuchen ein ausgereiftes Therapiekonzept zu entwickeln.
Zugleich beschreibt Masquelet et al. (2000) eine neue Technik, ein zweistufiges Verfahren zur Rekonstruktion von Knochendefekten. Es wird eine biologisch aktive Membran induziert, welche verschiedene Wachstumsfaktoren (wie z.B. VEGF, TGF beta1, BMP-2) sezerniert, die osteoinduktiv wirksam sind. Mit diesem operativen Verfahren wurden bereits gute klinische Ergebnisse bei Knochendefekten nach Tumorresektionen und Traumata erzielt.
Das Ziel dieser Studie ist es einen anorganischen Knochenersatzstoff von Heraeus Herafill unter Verwendung der induzierten Membrantechnik nach Masquelet am Rattenfemur zu testen. Die Forschung erfolgt dabei unter der Hypothese, dass die Korngröße des Knochenersatzmaterials Herafill in Kombination mit BMC-Besiedelung Einfluss auf die Heilung eines kritischen Knochendefekts hat.
Heterologously expressed genes require adaptation to the host organism to ensure adequate levels of protein synthesis, which is typically approached by replacing codons by the target organism’s preferred codons. In view of frequently encountered suboptimal outcomes we introduce the codon-specific elongation model (COSEM) as an alternative concept. COSEM simulates ribosome dynamics during mRNA translation and informs about protein synthesis rates per mRNA in an organism- and context-dependent way. Protein synthesis rates from COSEM are integrated with further relevant covariates such as translation accuracy into a protein expression score that we use for codon optimization. The scoring algorithm further enables fine-tuning of protein expression including deoptimization and is implemented in the software OCTOPOS. The protein expression score produces competitive predictions on proteomic data from prokaryotic, eukaryotic, and human expression systems. In addition, we optimized and tested heterologous expression of manA and ova genes in Salmonella enterica serovar Typhimurium. Superiority over standard methodology was demonstrated by a threefold increase in protein yield compared to wildtype and commercially optimized sequences.