Predicting H{\alpha} emission line galaxy counts for future galaxy redshift surveys

Knowledge of the number density of H$\alpha$ emitting galaxies is vital for assessing the scientific impact of the Euclid and WFIRST missions. In this work we present predictions from a galaxy formation model, Galacticus, for the cumulative number counts of H$\alpha$-emitting galaxies. We couple Galacticus to three different dust attenuation methods and examine the counts using each method. A $\chi^2$ minimisation approach is used to compare the model predictions to observed galaxy counts and calibrate the dust parameters. We find that weak dust attenuation is required for the Galacticus counts to be broadly consistent with the observations, though the optimum dust parameters return large values for $\chi^2$, suggesting that further calibration of Galacticus is necessary. The model predictions are also consistent with observed estimates for the optical depth and the H$\alpha$ luminosity function. Finally we present forecasts for the redshift distributions and number counts for two Euclid-like and one WFIRST-like survey. For a Euclid-like survey with redshift range $0.9\leqslant z\leqslant 1.8$ and H$\alpha+{\rm [NII]}$ blended flux limit of $2\times 10^{-16}{\rm erg}\,{\rm s}^{-1}\,{\rm cm}^{-2}$ we predict a number density between 3900--4800 galaxies per square degree. For a WFIRST-like survey with redshift range $1\leqslant z\leqslant 2$ and blended flux limit of $1\times 10^{-16}{\rm erg}\,{\rm s}^{-1}\,{\rm cm}^{-2}$ we predict a number density between 10400--15200 galaxies per square degree.Comment: 21 pages (including appendix), 12 figures, 6 tables. Accepted b

Integrating Syntactic and Prosodic Information for the Efficient Detection of Empty Categories

We describe a number of experiments that demonstrate the usefulness of prosodic information for a processing module which parses spoken utterances with a feature-based grammar employing empty categories. We show that by requiring certain prosodic properties from those positions in the input where the presence of an empty category has to be hypothesized, a derivation can be accomplished more efficiently. The approach has been implemented in the machine translation project VERBMOBIL and results in a significant reduction of the work-load for the parser.Comment: To appear in the Proceedings of Coling 1996, Copenhagen. 6 page

Risk factor analysis for fast track protocol failure

Background: The introduction of fast-track treatment procedures following cardiac surgery has significantly shortened hospitalisation times in intensive care units (ICU). Readmission to intensive care units is generally considered a negative quality criterion. The aim of this retrospective study is to statistically analyse risk factors and predictors for re-admission to the ICU after a fast-track patient management program. Methods: 229 operated patients (67 ± 11 years, 75% male, BMI 27 ± 3, 6/2010-5/2011) with use of extracorporeal circulation (70 ± 31 min aortic crossclamping, CABG 62%) were selected for a preoperative fast-track procedure (transfer on the day of surgery to an intermediate care (IMC) unit, stable circulatory conditions, extubated). A uni- and multivariate analysis were performed to identify independent predictors for re-admission to the ICU. Results: Over the 11-month study period, 36% of all preoperatively declared fast-track patients could not be transferred to an IMC unit on the day of surgery (n = 77) or had to be readmitted to the ICU after the first postoperative day (n = 4). Readmission or ICU stay signifies a dramatic worsening of the patient outcome (mortality 0/10%, mean hospital stay 10.3 ± 2.5/16.5 ± 16.3, mean transfusion rate 1.4 ± 1,7/5.3 ± 9.1). Predicators for failure of the fast-track procedure are a preoperative ASA class > 3, NYHA class > III and an operation time >267 min ± 74. The significant risk factors for a major postoperative event (= low cardiac output and/or mortality and/or renal failure and/or re-thoracotomy and/or septic shock and/or wound healing disturbances and/or stroke) are a poor EF (OR 2.7 CI 95% 0.98-7.6) and the described ICU readmission (OR 0.14 CI95% 0.05-0.36). Conclusion: Re-admission to the ICU or failure to transfer patients to the IMC is associated with a high loss of patient outcome. The ASA > 3, NYHA class > 3 and operation time >267 minutes are independent predictors of fast track protocol failure

Recent advances in the understanding of trimeric autotransporter adhesins

Adhesion is the initial step in the infection process of gram-negative bacteria. It is usually followed by the formation of biofilms that serve as a hub for further spread of the infection. Type V secretion systems engage in this process by binding to components of the extracellular matrix, which is the first step in the infection process. At the same time they provide protection from the immune system by either binding components of the innate immune system or by establishing a physical layer against aggressors. Trimeric autotransporter adhesins (TAAs) are of particular interest in this family of proteins as they possess a unique structural composition which arises from constraints during translocation. The sequence of individual domains can vary dramatically while the overall structure can be very similar to one another. This patchwork approach allows researchers to draw conclusions of the underlying function of a specific domain in a structure-based approach which underscores the importance of solving structures of yet uncharacterized TAAs and their individual domains to estimate the full extent of functions of the protein a priori. Here, we describe recent advances in understanding the translocation process of TAAs and give an overview of structural motifs that are unique to this class of proteins. The role of BpaC in the infection process of Burkholderia pseudomallei is highlighted as an exceptional example of a TAA being at the centre of infection initiation.Peer reviewe

Structural and functional elucidation of the trimeric autotransporter adhesin BpaC from Burkholderia pseudomallei

The trimeric autotransporter adhesin (TAA) BpaC plays a central role in the initial infection stages of the Gram-negative Burkholderia pseudomallei. The actual function of this protein on a biochemical level was undetermined at the start of this project. I endeavoured to identify binding partners of BpaC and associate the individual domains of the solvent-accessible part of the protein with specific binding events. To this end, I analysed the protein sequence using a combination of bioinformatic tools and TAA specific sequence rules to accurately determine secondary structure prevalences, domain borders, and likely binding partners. I designed, expressed, and purified multiple constructs of various lengths and composition, that all together cover the full solvent-accessible domain of BpaC, making every part of the protein accessible for functional or structural experiments. On a structural level, I solved parts of the C-terminal head domain of BpaC which, by extension, can be used to deduce the structural model of the full head domain. This model provided the basis for the introduction of a new subcategory of left-handed parallel beta-rolls named BpaC-like head domains; based on the unique surface charge properties of the C-terminal located head domain of BpaC. On a functional level, the identification of likely homology models for the individual domains of BpaC resulted in the prediction of binding partners of BpaC. Some of the candidates, namely extracellular matrix proteins from humans like fibronectin and collagen, were used in binding assays. These experiments revealed a preference of BpaC to bind to fibronectin, collagen I and collagen II. However, a clear domain-ligand association could not be determined. Lastly, a new hypothetical infection model is provided in which BpaC acts together with type I pili in the initial steps of adhesion of Burkholderia pseudomallei in a three stage process

The C-terminal head domain of Burkholderia pseudomallei BpaC has a striking hydrophilic core with an extensive solvent network

Gram-negative pathogens like Burkholderia pseudomallei use trimeric autotransporter adhesins such as BpaC as key molecules in their pathogenicity. Our 1.4 angstrom crystal structure of the membrane-proximal part of the BpaC head domain shows that the domain is exclusively made of left-handed parallel beta-roll repeats. This, the largest such structure solved, has two unique features. First, the core, rather than being composed of the canonical hydrophobic Ile and Val, is made up primarily of the hydrophilic Thr and Asn, with two different solvent channels. Second, comparing BpaC to all other left-handed parallel beta-roll structures showed that the position of the head domain in the protein correlates with the number and type of charged residues. In BpaC, only negatively charged residues face the solvent-in stark contrast to the primarily positive surface charge of the left-handed parallel beta-roll "type" protein, YadA. We propose extending the definitions of these head domains to include the BpaC-like head domain as a separate subtype, based on its unusual sequence, position, and charge. We speculate that the function of left-handed parallel beta-roll structures may differ depending on their position in the structure.Peer reviewe

Activation of the Catalytic Activity of Thrombin for Fibrin Formation by Ultrasound

The regulation of enzyme activity is a method to control biological function. We report two systems enabling the ultrasound-induced activation of thrombin, which is vital for secondary hemostasis. First, we designed polyaptamers, which can specifically bind to thrombin, inhibiting its catalytic activity. With ultrasound generating inertial cavitation and therapeutic medical focused ultrasound, the interactions between polyaptamer and enzyme are cleaved, restoring the activity to catalyze the conversion of fibrinogen into fibrin. Second, we used split aptamers conjugated to the surface of gold nanoparticles (AuNPs). In the presence of thrombin, these assemble into an aptamer tertiary structure, induce AuNP aggregation, and deactivate the enzyme. By ultrasonication, the AuNP aggregates reversibly disassemble releasing and activating the enzyme. We envision that this approach will be a blueprint to control the function of other proteins by mechanical stimuli in the sonogenetics field

Activation of the Catalytic Activity of Thrombin for Fibrin Formation by Ultrasound

The regulation of enzyme activity is a method to control biological function. We report two systems enabling the ultrasound-induced activation of thrombin, which is vital for secondary hemostasis. First, we designed polyaptamers, which can specifically bind to thrombin, inhibiting its catalytic activity. With ultrasound generating inertial cavitation and therapeutic medical focused ultrasound, the interactions between polyaptamer and enzyme are cleaved, restoring the activity to catalyze the conversion of fibrinogen into fibrin. Second, we used split aptamers conjugated to the surface of gold nanoparticles (AuNPs). In the presence of thrombin, these assemble into an aptamer tertiary structure, induce AuNP aggregation, and deactivate the enzyme. By ultrasonication, the AuNP aggregates reversibly disassemble releasing and activating the enzyme. We envision that this approach will be a blueprint to control the function of other proteins by mechanical stimuli in the sonogenetics field. © 2021 The Authors. Angewandte Chemie International Edition published by Wiley-VCH Gmb

Effects of dietary yeast inclusion and acute stress on post-prandial whole blood profiles of dorsal aorta-cannulated rainbow trout

Yeast is a potential alternative to fish meal in diets for farmed fish, yet replacing more than 50 % of fish meal results in reduced fish growth. In a 4-week experiment, 15 rainbow trout (Oncorhynchus mykiss) were cannulated and fed three diets each week: 30 % fish meal as a control (FM); 60 % replacement of fish meal protein, on a digestible basis, with Saccharomyces cerevisiae (SC); and 60 % replacement with Wickerhamomyces anomalus and S. cerevisiae mix (WA). Blood was collected at 0, 3, 6, 12 and 24 h after feeding. In the final week, fish were exposed to a 1-min netting stressor to evaluate possible diet-stress interactions. Significant increases in pH, TCO2, HCO3 and base excess were found after fish were fed the SC and WA diets compared with FM, which elevated blood alkaline tides. Yeast ingredients had lower buffering capacity and ash content than fish meal, which explained the increase in alkaline tides. In addition, fish fed the WA diet had significantly reduced erythrocyte area and fish fed SC and WA diets had increased mean corpuscular haemoglobin levels, indicating haemolytic anaemia. Higher levels of nucleic acid in yeast-based diets and potentially higher production of reactive oxygen species were suspected of damaging haemoglobin, which require replacement by smaller immature erythrocytes. Acute stress caused the expected rise in cortisol and glucose levels, but no interaction with diet was found. These results show that replacing 60 % of fish meal protein with yeasts can induce haemolytic anaemia in rainbow trout, which may limit yeast inclusion in diets for farmed fish