Strategies To Design Selective Histone Deacetylase Inhibitors

This review classifies drug-design strategies successfully implemented in the development of histone deacetylase (HDAC) inhibitors, which have many applications including cancer treatment. Our focus is on especially demanded selective HDAC inhibitors and their structure-activity relationships in relation to corresponding protein structures. The main part of the paper is divided into six subsections each narrating how optimization of one of six structural features can influence inhibitor selectivity. It starts with the impact of the zinc binding group on selectivity, continues with the optimization of the linker placed in the substrate binding tunnel as well as the adjustment of the cap group interacting with the surface of the protein, and ends with the addition of groups targeting class-specific sub-pockets: the side-pocket-, lower-pocket- and foot-pocket-targeting groups. The review is rounded off with a conclusion and an outlook on the future of HDAC inhibitor design.     

Production of bioactive proteins and peptides from the diatom Nitzschia laevis and comparison of their in vitro antioxidant activities with those from Spirulina platensis and Chlorella vulgaris

This research focuses on green production of bioactive proteins and hydrolysates from Nitzschia. A comparison of antioxidant activities was established between protein extracts and hydrolysates from Nitzschia and two other well‐known microalgae, chlorella and spirulina. Protein hydrolysates from these microalgae were produced using Alcalase^®, Flavourzyme^® and Trypsin. The hydrolysis process enhanced the antioxidant activities in general, especially those obtained using Alcalase^®. Nitzschia showed the highest (P < 0.05) total phenolic content/reducing capacity (2.4 ± 0.02 mg GAE/100 g) after 90 min of hydrolysis with Alcalase^®. The ABTS [2,2′‐Azino‐bis(3‐ethylbenzothiazoline‐6‐sulphonic acid)] radical scavenging activity (66.77 ± 0.00%) was highest (P < 0.05) after 120 min of hydrolysis, but DPPH (2,2‐Diphenyl‐1‐picrylhydrazyl radical) was low (29.59 ± 0.02%). A correlation between ABTS activity and total phenolic contents was the highest (P < 0.05) for protein hydrolysates from all three organisms using Alcalase^®, but superoxide anion radical scavenging activity was intermediate for Nitzschia. Therefore, Nitzschia protein hydrolysates have the potential to be used as antioxidants.     

Should medium-sized contractors still implement home-made information technologies on construction sites?

Despite the increasing dissemination of the Building Information Modeling (BIM) approach, many firms are still far from BIM and are only starting to adopt information technologies. We conducted an ethnographic action research with an industrial partner that implements information technologies on its construction sites, with a strong preference for home-made applications. Results show that the development of such applications faces difficulties and that multiple iterations and versions are necessary before achieving the expected goals because the required competencies are lacking among internal development teams. Moreover, initial needs evolve considerably throughout the application’s development and evaluation process. However, notwithstanding the difficulties encountered during the different application development phases, the industrial partner believes the decision to be worthwhile because of the desire to have internal control over the project data and the need to consider certain specificities related to business processes.     

Mediated Electrochemistry to Mimic Biology's Oxidative Assembly of Functional Matrices

Biology uses diffusible oxidants to perform functions that range from signaling to matrix assembly, and these oxidation chemistries offer surprising selectivities. Here, it is reported that mediated electrochemistry can access the richness of such oxidation chemistries. Specifically, electrode‐imposed voltage inputs are used to locally generate oxidized mediators that can diffuse into polymer solutions and induce the formation of covalent bonds for the deposition and functionalization of hydrogels at the electrode surface. Depending on the mediator's redox potential (E⁰), it is possible to “gate” the voltage inputs to target specific residues (e.g., thiols or amines) and oxidation chemistries. Further, mediators of varying E⁰ offer different reactivities and thus allow control of reaction‐diffusion rates to modulate the hydrogel's crosslink density and mechanical properties. Importantly, this mediated oxidation can be performed under physiologically relevant conditions to preserve labile biological functionalities (e.g., cell viability and protein function). Finally, it is demonstrated that protein fusion tags can be engineered to have “targetable” amino acid residues that enable protein function to be oxidatively conjugated to electrodeposited hydrogels. In summary, mediated electrochemistry can engage orthogonal oxidation chemistries to create functionalized matrices and thus mediated electrochemistry should add important capabilities to the electrofabrication toolbox.     

Traffic, transportation, infrastructure and externalities A theoretical framework for a CGE analysis

In Europe traffic congestions make it impossible to estimate travel time. The increasing number of cars calls for a transportation policy towards an improved efficiency of the transportation system. However, extending road infrastructure to reduce the congestion externality implies another type of externality, air pollution. Designing a transportation policy in industrialized countries one has to consider this trade-off. Our objective is to investigate the role of transportation services and their pricces within an interindustry framework. The authority wishes to minimize total cost of production with respect to the provision of infrastructure subject to an emission standard. By omitting a financial constraint to finance infrastructure we determine the size of infrastructure where no congestion occurs. The productivity effect of infrastructure and the cost savings from a dissolved congestion determine the optimal stock of infrastructure. Our congestion index is unity in that case of no financial constraint. If the extension of infrastructure has to be paid for by taxation, we obtain a lower level of infrastructure. In view of the trade-off between the benefit of a productivity gain from a dissolved congestion and the deadweight loss from taxation this lower level of infrastructure will result in an index of congestion higher than unity, implying a negative externality to the economy. Received: June 1996 / Accepted: February 1997     

Biodegradability and ecotoxicity of commercially available geothermal heat transfer fluids

Commercially available heat transfer fluids used in borehole heat exchangers were investigated for their composition, their biodegradability as well as their ecotoxicity. The main components of the fluids are organic compounds (often glycols) for freezing protection. Biodegradation of the fluids in laboratory studies caused high oxygen depletion as well as nitrate/iron(III) reduction under anaerobic conditions. Additives such as benzotriazoles for corrosion protection were persistent. Ecotoxicity data show that the commercially available fluids caused much higher ecotoxicity than their main organic constituents. Consequently, with regard to groundwater protection pure water as heat transfer medium is recommended. The second best choice is the usage of glycols without any additives. Effects on groundwater quality should be considered during ecological-economical cost-benefit-analyses of further geothermal energy strategies. The protection of groundwater as the most important drinking water resource must take priority over the energy gain from aquifers.     

Piecewise empirical model (PEM) of resistive memory for pulsed analog and neuromorphic applications

With the end of Dennard scaling and the ever-increasing need for more efficient, faster computation, resistive switching devices (ReRAM), often referred to as memristors, are a promising candidate for next generation computer hardware. These devices show particular promise for use in an analog neuromorphic computing accelerator as they can be tuned to multiple states and be updated like the weights in neuromorphic algorithms. Modeling a ReRAM-based neuromorphic computing accelerator requires a compact model capable of correctly simulating the small weight update behavior associated with neuromorphic training. These small updates have a nonlinear dependence on the initial state, which has a significant impact on neural network training. Consequently, we propose the piecewise empirical model (PEM), an empirically derived general purpose compact model that can accurately capture the nonlinearity of an arbitrary two-terminal device to match pulse measurements important for neuromorphic computing applications. By defining the state of the device to be proportional to its current, the model parameters can be extracted from a series of voltages pulses that mimic the behavior of a device in an analog neuromorphic computing accelerator. This allows for a general, accurate, and intuitive compact circuit model that is applicable to different resistance-switching device technologies. In this work, we explain the details of the model, implement the model in the circuit simulator Xyce, and give an example of its usage to model a specific \(\hbox {Ta}/\hbox {TaO}_{\mathrm{x}}\) device.     

Selecting and assessing challenge problems

Abstract

Organisations conducting research programs often focus the work of their scientists and technologists on challenge problems (CPs). These challenges are designed to ensure that progress is measurable and relevant to the goals of the program sponsor. Generating and selecting pertinent CPs is difficult, as is assessing their value. We describe a method of generating and selecting CPs and its application in a highly collaborative, multi-organisation research program. Thirty-eight biologists, chemists, mathematicians and computer scientists across academic, commercial and government organisations generated and ranked their top choices from among 12 richly described candidate challenge problems. A ranked-choice voting formula was applied. Five CPs were highly scored; the remaining seven were distributed across a lower range of scores. The program sponsor subsequently directed researchers to address six CPs, including the elected five. Analysis of the rationales that participants offered for their CP rankings revealed four domain-independent dimensions of value: capability, speed, impact and synergy. These dimensions of value can help managers of interdisciplinary research programs systematically select a portfolio of CPs that will efficiently apply utilise resources towards program goals and facilitate measurement of scientific progress.