Non-linear matrix modeling of forest growth with permanent plot data: The case of uneven-aged Douglas-fir stands

Uneven‐aged forest management is acquiring increasing importance throughout the world as an alternative to clear cutting. Simple stage‐structured matrix models can be used to predict the growth of uneven‐aged stands, and they are easily incorporated in optimization analysis. Parameters of these models can be estimated from readily available permanent plot data. Such a growth and yield model is presented for mixed, uneven‐aged Douglas‐fir and hardwood stands. The model was calibrated with data from 66 permanent plots in Oregon and Washington. The density‐dependent matrix model predicts the number of trees by diameter class and species type, softwood or hardwood. The parameters are based on individual tree growth equations, individual tree mortality equations, and stand ingrowth equations. The individual tree equations are a function of tree diameter, stand density, species, and site index. The stand‐level ingrowth equations are a function of stand density. The model was validated in the short term by comparing the number of trees in each diameter and species class at the time of the second inventory with the number predicted by the model, given conditions at the first inventory. A long‐term validation of the model was also done by comparing the steady‐state stand structure and stand volume with those observed for old‐growth stands. The model was applied to show the effects of different cutting cycles on productivity, diversity of tree species and size, and financial returns. The results suggest that uneven‐aged management of the Douglas‐fir forest type in the Pacific Northwest can be as productive as even‐aged management, with the added benefits of continuous cover forestry.     

A 3D shape segmentation approach for robot grasping by parts

Neuro-psychological findings have shown that human perception of objects is based on part decomposition. Most objects are made of multiple parts which are likely to be the entities actually involved in grasp affordances. Therefore, automatic object recognition and robot grasping should take advantage from 3D shape segmentation. This paper presents an approach toward planning robot grasps across similar objects by part correspondence. The novelty of the method lies in the topological decomposition of objects that enables high-level semantic grasp planning.In particular, given a 3D model of an object, the representation is initially segmented by computing its Reeb graph. Then, automatic object recognition and part annotation are performed by applying a shape retrieval algorithm. After the recognition phase, queries are accepted for planning grasps on individual parts of the object. Finally, a robot grasp planner is invoked for finding stable grasps on the selected part of the object. Grasps are evaluated according to a widely used quality measure. Experiments performed in a simulated environment on a reasonably large dataset show the potential of topological segmentation to highlight candidate parts suitable for grasping.     

Model Checking Linear Programs with Arrays

In previous work we proposed Linear Programs as a fine grained model for imperative programs, and showed how the model checking procedure used in SLAM can be generalised to a model checking procedure for Linear Programs. In this paper we show that our model checking procedure for linear programs can be extended in such a way to support the analysis of linear programs featuring a symbol for undefined values and conditional expressions. This extension is particularly important as it paves the way to the construction of model checking procedures for wider classes of imperative programs such as, e.g., linear programs with arrays. We provide a detailed account of a symbolic model checking procedure for this extended class of linear programs, discuss its implementation in the eureka tool, and present experimental results that confirm its effectiveness in the analysis of linear programs with arrays.     

Experimental methods in chemical engineering: Process simulation

Process simulation software designs equipment, simulates operations, optimizes a plant's configuration (heat exchangers network, for example), estimates operating and capital expenses, and serves as an educational tool. However, mastering the theoretical background minimizes common mistakes such as applying an incorrect thermodynamic method, selecting improper algorithms in the case of tear systems, and setting irrational system specifications. Engineers and researchers will exploit this tool more often in the future as constant advancements in simulation science as well as new models are released continually. Process simulators make it easier to build digital twins and thus will facilitate the implementation of the industry 4.0 guidelines. We highlight the mathematical and technical features of process simulators, as well as the capabilities and the fields of application. A bibliometric map of keywords from articles citing Aspen+, Aspen plus, Hysys, and Pro/II indexed by Web of Science between 2017 and 2020 identified the main research clusters, such as design, optimization, energy or exergy, biomass; H₂ and CO₂ capture, thermodynamics; and separations and techno-economic analysis.     

Two‐Color Emitting Colloidal Nanocrystals as Single‐Particle Ratiometric Probes of Intracellular pH

Intracellular pH is a key parameter in many biological mechanisms and cell metabolism and is used to detect and monitor cancer formation and brain or heart diseases. pH‐sensing is typically performed by fluorescence microscopy using pH‐responsive dyes. Accuracy is limited by the need for quantifying the absolute emission intensity in living biological samples. An alternative with a higher sensitivity and precision uses probes with a ratiometric response arising from the different pH‐sensitivity of two emission channels of a single emitter. Current ratiometric probes are complex constructs suffering from instability and cross‐readout due to their broad emission spectra. Here, we overcome such limitations using a single‐particle ratiometric pH probe based on dot‐in‐bulk CdSe/CdS nanocrystals (NCs). These nanostructures feature two fully‐separated narrow emissions with different pH sensitivity arising from radiative recombination of core‐ and shell‐localized excitons. The core emission is nearly independent of the pH, whereas the shell luminescence increases in the 3–11 pH range, resulting in a cross‐readout‐free ratiometric response as strong as 600%. In vitro microscopy demonstrates that the ratiometric response in biologic media resembles the precalibralation curve obtained through far‐field titration experiments. The NCs show good biocompatibility, enabling us to monitor in real‐time the pH in living cells.     

Pathological ATX3 Expression Induces Cell Perturbations in E. coli as Revealed by Biochemical and Biophysical Investigations

Amyloid aggregation of human ataxin-3 (ATX3) is responsible for spinocerebellar ataxia type 3, which belongs to the class of polyglutamine neurodegenerative disorders. It is widely accepted that the formation of toxic oligomeric species is primarily involved in the onset of the disease. For this reason, to understand the mechanisms underlying toxicity, we expressed both a physiological (ATX3-Q24) and a pathological ATX3 variant (ATX3-Q55) in a simplified cellular model, Escherichia coli. It has been observed that ATX3-Q55 expression induces a higher reduction of the cell growth compared to ATX3-Q24, due to the bacteriostatic effect of the toxic oligomeric species. Furthermore, the Fourier transform infrared microspectroscopy investigation, supported by multivariate analysis, made it possible to monitor protein aggregation and the induced cell perturbations in intact cells. In particular, it has been found that the toxic oligomeric species associated with the expression of ATX3-Q55 are responsible for the main spectral changes, ascribable mainly to the cell envelope modifications. A structural alteration of the membrane detected through electron microscopy analysis in the strain expressing the pathological form supports the spectroscopic results.     

Predicting Intentions from Motion: The Subject-Adversarial Adaptation Approach

International Journal of Computer Vision - This paper aims at investigating the action prediction problem from a pure kinematic perspective. Specifically, we address the problem of recognizing...     

A DNA‐Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition

A DNA‐encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5‐bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a K_d value of 6 nm , while compounds with the same substituents on an equidistant but flexible l ‐lysine scaffold showed 140‐fold lower affinity. A 18 nm tankyrase‐1 binder featured l ‐lysine as linking moiety, while molecules based on d ‐Lysine or (2S,4S)‐amino‐l ‐proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.     

Biosynthesis and spectroscopic characterization of 2-TM fragments encompassing the sequence of a human GPCR, the Y4 receptor

This paper presents a divide‐and‐conquer approach towards obtaining solution structures of G protein‐coupled receptors. The human Y4 receptor was dissected into two to three transmembrane helix fragments, which were individually studied by solution NMR. We systematically compared various biosynthetic routes for the expression of the fragments in Escherichia coli and discuss purification strategies. In particular, we have compared the production of transmembrane (TM) fragments as inclusion bodies by using the ΔTrp leader sequence, with membrane‐directed expression by using Mistic as the fusion partner, and developed methods for enzymatic cleavage. In addition, direct expression of two‐TM fragments into inclusion bodies is a successful route in some cases. With the exception of TM13, we could produce all fragments in isotope‐labeled form in quantities sufficient for NMR studies. Almost complete backbone resonance assignment was obtained for the first two helices, as well as for helices 5 and 7, and a high degree was obtained for TM6, while conformational exchange processes resulted in the disappearance of many signals from TM4. In addition, complete assignments were obtained for all residues of the N‐terminal domain, as well as the extracellular and cytosolic loops (with the exception of an undecapeptide segment in the second extracellular loop, EC2) and for the complete cytosolic C‐terminal tail. In total, backbone resonances of 78 % of all residues were assigned for the Y4 receptor. Predictions of secondary structure based on backbone chemical shifts indicate that most residues from the TM regions adopt helical conformations, with exception of those around polar residues or prolines. However, the domain boundaries differ slightly from those predicted for homology models. We suggest that the obtained chemical shifts might be useful in assigning the full‐length receptor.