Xylan oligosaccharides and cellobiohydrolase I (TrCel7A) interaction and effect on activity

<p>Abstract</p> <p>Background</p> <p>The well-studied cellulase mixture secreted by <it>Trichoderma reesei </it>(anamorph to <it>Hypocrea jecorina</it>) contains two cellobiohydolases (CBHs), cellobiohydrolase I (<it>Tr</it>Cel7A) and cellobiohydrolase II (<it>Tr</it>CeI6A), that are core enzymes for the solubilisation of cellulose. This has attracted significant research interest because of the role of the CBHs in the conversion of biomass to fermentable sugars. However, the CHBs are notoriously slow and susceptible to inhibition, which presents a challenge for the commercial utilisation of biomass. The xylans and xylan fragments that are also present in the biomass have been suggested repeatedly as one cause of the reduced activity of CHBs. Yet, the extent and mechanisms of this inhibition remain poorly elucidated. Therefore, we studied xylan oligosaccharides (XOSs) of variable lengths with respect to their binding and inhibition of both <it>Tr</it>Cel7A and an enzyme variant without the cellulose-binding domain (CBM).</p> <p>Results</p> <p>We studied the binding of XOSs to <it>Tr</it>Cel7A by isothermal titration calorimetry. We found that XOSs bind to <it>Tr</it>Cel7A and that the affinity increases commensurate with XOS length. The CBM, on the other hand, did not affect the affinity significantly, which suggests that XOSs may bind to the active site. Activity assays of <it>Tr</it>Cel7A clearly demonstrated the negative effect of the presence of XOSs on the turnover number.</p> <p>Conclusions</p> <p>On the basis of these binding data and a comparison of XOS inhibition of the activity of the two enzyme variants towards, respectively, soluble and insoluble substrates, we propose a competitive mechanism for XOS inhibition of <it>Tr</it>Cel7A with phosphoric swollen cellulose as a substrate.</p

Ageing in bosonic particle-reaction models with long-range transport

Ageing in systems without detailed balance is studied in bosonic contact and pair-contact processes with Levy diffusion. In the ageing regime, the dynamical scaling of the two-time correlation function and two-time response function is found and analysed. Exact results for non-equilibrium exponents and scaling functions are derived. The behaviour of the fluctuation-dissipation ratio is analysed. A passage time from the quasi-stationary regime to the ageing regime is defined, in qualitative agreement with kinetic spherical models and p-spin spherical glasses.Comment: Latex2e, 24 pages, with 9 figures include

Graph Orientation and Flows Over Time

Flows over time are used to model many real-world logistic and routing problems. The networks underlying such problems -- streets, tracks, etc. -- are inherently undirected and directions are only imposed on them to reduce the danger of colliding vehicles and similar problems. Thus the question arises, what influence the orientation of the network has on the network flow over time problem that is being solved on the oriented network. In the literature, this is also referred to as the contraflow or lane reversal problem. We introduce and analyze the price of orientation: How much flow is lost in any orientation of the network if the time horizon remains fixed? We prove that there is always an orientation where we can still send $\frac{1}{3}$ of the flow and this bound is tight. For the special case of networks with a single source or sink, this fraction is $\frac12$ which is again tight. We present more results of similar flavor and also show non-approximability results for finding the best orientation for single and multicommodity maximum flows over time

On the Localization of Ultrasound Image Slices within Point Distribution Models

Thyroid disorders are most commonly diagnosed using high-resolution Ultrasound (US). Longitudinal nodule tracking is a pivotal diagnostic protocol for monitoring changes in pathological thyroid morphology. This task, however, imposes a substantial cognitive load on clinicians due to the inherent challenge of maintaining a mental 3D reconstruction of the organ. We thus present a framework for automated US image slice localization within a 3D shape representation to ease how such sonographic diagnoses are carried out. Our proposed method learns a common latent embedding space between US image patches and the 3D surface of an individual's thyroid shape, or a statistical aggregation in the form of a statistical shape model (SSM), via contrastive metric learning. Using cross-modality registration and Procrustes analysis, we leverage features from our model to register US slices to a 3D mesh representation of the thyroid shape. We demonstrate that our multi-modal registration framework can localize images on the 3D surface topology of a patient-specific organ and the mean shape of an SSM. Experimental results indicate slice positions can be predicted within an average of 1.2 mm of the ground-truth slice location on the patient-specific 3D anatomy and 4.6 mm on the SSM, exemplifying its usefulness for slice localization during sonographic acquisitions. Code is publically available: \href{https://github.com/vuenc/slice-to-shape}{https://github.com/vuenc/slice-to-shape}Comment: ShapeMI Workshop @ MICCAI 2023; 12 pages 2 figure

Gravity waves and the LHC: Towards high-scale inflation with low-energy SUSY

It has been argued that rather generic features of string-inspired inflationary theories with low-energy supersymmetry (SUSY) make it difficult to achieve inflation with a Hubble scale H > m_{3/2}, where m_{3/2} is the gravitino mass in the SUSY-breaking vacuum state. We present a class of string-inspired supergravity realizations of chaotic inflation where a simple, dynamical mechanism yields hierarchically small scales of post-inflationary supersymmetry breaking. Within these toy models we can easily achieve small ratios between m_{3/2} and the Hubble scale of inflation. This is possible because the expectation value of the superpotential relaxes from large to small values during the course of inflation. However, our toy models do not provide a reasonable fit to cosmological data if one sets the SUSY-breaking scale to m_{3/2} < TeV. Our work is a small step towards relieving the apparent tension between high-scale inflation and low-scale supersymmetry breaking in string compactifications.Comment: 21+1 pages, 5 figures, LaTeX, v2: added references, v3: very minor changes, version to appear in JHE

D-brane potentials in the warped resolved conifold and natural inflation

In this paper we obtain a model of Natural Inflation from string theory with a Planckian decay constant. We investigate D-brane dynamics in the background of the warped resolved conifold (WRC) throat approximation of Type IIB string compactifications on Calabi-Yau manifolds. When we glue the throat to a compact bulk Calabi-Yau, we generate a D-brane potential which is a solution to the Laplace equation on the resolved conifold. We can exactly solve this equation, including dependence on the angular coordinates. The solutions are valid down to the tip of the resolved conifold, which is not the case for the more commonly used deformed conifold. This allows us to exploit the effect of the warping, which is strongest at the tip. We inflate near the tip using an angular coordinate of a D5-brane in the WRC which has a discrete shift symmetry, and feels a cosine potential, giving us a model of Natural Inflation, from which it is possible to get a Planckian decay constant whilst maintaining control over the backreaction. This is because the decay constant for a wrapped brane contains powers of the warp factor, and so can be made large, while the wrapping parameter can be kept small enough so that backreaction is under control.Comment: 41 pages, 3 appendices, 1 figure, PDFLaTex; various clarifications added along with a new appendix on b-axions and wrapped D5 branes;version matches the one published in JHE

S3M: Scalable Statistical Shape Modeling through Unsupervised Correspondences

Statistical shape models (SSMs) are an established way to represent the anatomy of a population with various clinically relevant applications. However, they typically require domain expertise, and labor-intensive landmark annotations to construct. We address these shortcomings by proposing an unsupervised method that leverages deep geometric features and functional correspondences to simultaneously learn local and global shape structures across population anatomies. Our pipeline significantly improves unsupervised correspondence estimation for SSMs compared to baseline methods, even on highly irregular surface topologies. We demonstrate this for two different anatomical structures: the thyroid and a multi-chamber heart dataset. Furthermore, our method is robust enough to learn from noisy neural network predictions, potentially enabling scaling SSMs to larger patient populations without manual segmentation annotation.Comment: Accepted at MICCAI 2023. 13 pages, 6 figure

A novel, aerosol-nanocrystal floating-gate device for non-volatile memory applications

This paper describes the fabrication, and structural and electrical characterization of a new, aerosol-nanocrystal floating-gate FET, aimed at non-volatile memory (NVM) applications. This aerosol-nanocrystal NVM device features program/erase characteristics comparable to conventional stacked gate NVM devices, excellent endurance (>l0^5 P/E cycles), and long-term non-volatility in spite of a thin bottom oxide (55-60Å). In addition, a very simple fabrication process makes this aerosol-nanocrystal NVM device a potential candidate for low cost NVM applications