A 2-set-up Routley-Meyer Semantics for the 4-valued Relevant Logic E4

The logic BN4 can be considered as the 4-valued logic of the relevant conditional and the logic E4, as the 4-valued logic of (relevant) entailment. The aim of this paper is to endow E4 with a 2-set-up Routley-Meyer semantics. It is proved that E4 is strongly sound and complete w.r.t. this semantics

iMODS: internal coordinates normal mode analysis server

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animationś and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies.Human Frontier Science Program—RGP0039/2008, Ministerio de Economía y Competitividad—BFU2013-44306P and Comunidad de Madrid—CAM-S2010/BMD

RCD+: Fast Loop Modeling Server

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 angstrom for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained similar to 10-fold faster

Relational semantics for the 4-valued relevant logics BN4 and E4

The logic BN4 was defined by R.T. Brady in 1982. It can be considered as the 4-valued logic of the relevant conditional. E4 is a variant of BN4 that can be considered as the 4-valued logic of (relevant) entailment. The aim of this paper is to define reduced general Routley-Meyer semantics for BN4 and E4. It is proved that BN4 and E4 are strongly sound and complete w.r.t. their respective semantics

Synthesis of 3-alkyl enol mimics inhibitors of type II dehydroquinase: factors influencing their inhibition potency

Several 3-alkylaryl mimics of the enol intermediate in the reaction catalyzed by type II dehydroquinase were synthesized to investigate the effect on the inhibition potency of replacing the oxygen atom in the side chain by a carbon atom. The length and the rigidity of the spacer was also studied. The inhibitory properties of the reported compounds against type II dehydroquinase from Mycobacterium tuberculosis and Helicobacter pylori are also reported. The binding modes of these analogs in the active site of both enzymes were studied by molecular docking using GOLD 5.0 and dynamic simulations studiesFinancial support from the Xunta de Galicia (10PXIB2200122PR and GRC2010/12) and the Spanish Ministry of Science and Innovation (SAF2010-15076) is gratefully acknowledged. BB, AS and AP thank the Spanish Ministry of Science and Innovation for FPU fellowshipsS

Bringing Light to Science Undergraduate Students: A Successful Laboratory Experiment Illustrating the Principles and Applications of Bioluminescence

Although many laboratory experiments are available to illustrate spectrophotometric or fluorometric methods, few of them introduce the use of luminometry to students. Bioluminescence, a subtype of chemiluminescence, is produced when an enzyme-catalyzed chemical reaction gives rise to light emission. Despite the advantages of bioluminescent methods, including sensitivity and specificity, and their increasing use in experimental sciences and biomedical laboratories, their presence in courses is almost nonexistent. The luciferase-catalyzed enzymatic reaction has generated a myriad of practical applications, including those derived from the measurement of the ATP consumed in the reaction. In particular, the measurement of ATP levels in drinking or stored waters directly correlates with their bacteria content, facilitating the development of rapid methods for detecting bacterial contamination. This avoids the long waiting time associated with traditional microbiological methods, based on the growth of the microorganisms in a suitable culture medium. Over the past two years at the University of Malaga, we have implemented a new laboratory experiment for undergraduate chemistry and biochemistry students. In this experiment, students detected bacterial contamination in water by quantifying ATP with the luciferase-catalyzed reaction. The experiment was successfully implemented in two different formats, either as a full project developed by students throughout the entire duration of the academic course, or as a short protocol, carried out in a single laboratory session. Between them, a whole range of intermediate options could be arranged by educators to suit their course requirements and the learning objectives to be achieved by students.This work was supported by the University of Malaga (Spain) funds granted to the educational innovation projects PIE19-086 and PIE19-057, and the Spanish Ministry of Science, Innovation and Universities Grant EDU2017-82197-P

Exploring the Water-Binding Pocket of the Type II Dehydroquinase Enzyme in the Structure-Based Design of Inhibitors

Structural and computational studies to explore the WAT1 binding pocket in the structure-based design of inhibitors against the type II dehydroquinase (DHQ2) enzyme are reported. The crystal structures of DHQ2 from M. tuberculosis in complex with four of the reported compounds are described. The electrostatic interaction observed between the guanidinium group of the essential arginine and the carboxylate group of one of the inhibitors in the reported crystal structures supports the recently suggested role of this arginine as the residue that triggers the release of the product from the active site. The results of the structural and molecular dynamics simulation studies revealed that the inhibitory potency is favored by promoting interactions with WAT1 and the residues located within this pocket and, more importantly, by avoiding situations where the ligands occupy the WAT1 binding pocket. The new insights can be used to advantage in the structure-based design of inhibitorsFinancial support from the Spanish Ministry of Science and Innovation (Grant SAF2010-15076) and the Xunta de Galicia (Grant GRC2013/041) is gratefully acknowledged. B.B. and A.P. thank the Spanish Ministry of Education for their respective FPU fellowships. A.S. thanks the Spanish Ministry of Economy and Competitiveness for her FPI fellowship. J.M.O. thanks the Xunta de Galicia for a Plan I2C postdoctoral fellowshipS

Interaction with touchscreen smartphones in patientswith essential tremor and healthy individuals.

tremorAbstractIntroduction: Smartphone use in biomedical research is becoming more prevalent in differ-ent clinical settings. We performed a pilot study to obtain information on smartphone use bypatients with essential tremor (ET) and healthy controls, with a view to determining whetherperformance of touchscreen tasks is different between these groups and describing touchscreeninteraction factors.Method: A total of 31 patients with ET and 40 sex- and age-matched healthy controls com-pleted a descriptive questionnaire about the use of smartphones. Participants subsequentlyinteracted with an under-development Android application, and performed 4 tests evaluatingtypical touchscreen interaction gestures; each test was performed 5 times.Result: The type of smartphone use and touchscreen interaction were not significantly differ-ent between patients and controls. Age and frequency of smartphone use are key factors intouchscreen interaction.Conclusion: Our results support the use of smartphone touchscreens for research into ET,although further studies are required.pre-print1030 K

Mortality due to COVID-19 in Spain and its association with environmental factors and determinants of health

The objective of this study was to identify which air pollutants, atmospheric variables and health determinants could infuence COVID-19 mortality in Spain. This study used information from 41 of the 52 provinces in Spain (from Feb. 1, to May 31, 2021). Generalized Linear Models (GLM) with Poisson link were carried out for the provinces, using the Rate of Mortality due to COVID-19 (CM) per 1,000,000 inhabitants as dependent variables, and average daily concentrations of PM10 and NO2 as independent variables. Meteorological variables included maximum daily temperature (Tmax) and average daily absolute humidity (HA). The GLM model controlled for trend, seasonalities and the autoregressive character of the series. Days with lags were established. The relative risk (RR) was calculated by increases of 10 g/m3 in PM10 and NO2 and by 1 ℃ in the case of Tmax and 1 g/m3 in the case of HA. Later, a linear regression was carried out that included the social determinants of health.The authors would like to thank the Carlos III Health Institute for their fnancial support Project ENPY 221/20. This work was carried out with funds of the ENPY 221/20 project

Three decades of remote sensing analysis of forest decline related to climate change

Climate change is predicted to lead to increasingly intense and hotter droughts, causing physiological weakness followed by forest decline in many regions of the world. Long- and short-range remote sensing (satellites and unmanned aerial vehicles, commonly called drones) can sense drought-induced changes in vegetation. Although several studies have addressed forest decline events, none have analyzed the forest decline attributable to climate change using remote sensing in a concise manner. A bibliometric analysis was carried out to characterize the scientific production reported in the Web of Science repository. The search descriptors were a combination of keywords related to forest decline and remote sensing. The results showed 278 articles published between 1989 and 2021 in 92 journals, with an average annual increase of 31%. A total of 29 nodes and 220 scientific collaboration links were located, mainly led by researchers from USA, Germany and China. Keyword analysis using World-TreeMap reflected the association of different key forest decline phenomena such as drought stress and climate change. Although the use of satellite information to study and understand forest decline has been reported for just over three decades, the most notable feature of the present research was the limited role of drones with only 5 studies. This reveals an area of opportunity to take advantage of the main strengths of drones, i.e., spatial and temporal resolution, low cost compared to manned flights, and centimeter accuracy. Therefore, it is strongly recommended to increase studies to improve the use of multispectral sensors, thermal and LiDAR technology for long-term monitoring of forest decline related to climate change