Virtual Log Research Articles

AN ALGORITHM FOR CALCULATING THE STEREO FACTOR

Information on wood volume is essential in forestry activities, especially in the sale of wood products. However, measuring solid volume during a harvest period is challenging. The viable parameter for measurement is stereo volume, which refers to the stacked quantity of wood, including the empty spaces between the logs. However, the stereo volume–cubic volume (solid) ratio, which is influenced by the taper, uniformity, and size of the trees, needs to be obtained. In most cases, if a field tester does not choose a reference value, the result is less than reliable. In this work, an algorithm is presented that estimates the stereo–cubic volume relationship from forest inventory and tree stacking data. It was implemented in Visual Basic for Applications (VBA) to simulate virtual log stacking. Its accuracy was evaluated in three field trials: the first and second in a eucalyptus stand and the third in a bamboo stand. Implementing the three calculation methods, the errors ranged from -12.34 to 8.33% for the cubing factor and from -8.94 to 15.64% for the stacking factor, which was the first degree of reliability for a parameter that requires a high level of accuracy because of the impact on wood buying and selling. The algorithm is easy to use but needs further validation in forest harvesting areas.

The VEGA web service: multipurpose online tools for molecular modelling and docking analyses.

The paper presents the VEGA Online web service, which includes a set of freely available tools deriving from the development of the VEGA suite of programs. In detail, the paper is focused on two tools: the VEGA Web Edition (WE) and the Score tool. The former is a versatile file format converter including relevant features for 2D/3D conversion, for surface mapping and for editing/preparing input files. The Score application allows rescoring docking poses and in particular includes the MLP Interactions Scores (MLPInS) for describing hydrophobic interactions. To the best of our knowledge, this web service is the only available resource by which one can calculate both the virtual log P of a given input molecule according to the MLP approach plus the corresponding MLP surface.

Volumetric yield coefficient: the key to regulating virtual credits for Amazon wood

ABSTRACT In Brazil, all transport and storage of native forest products and by-products must be registered within the DOF (Document of Forestry Origin) system. This computerized platform exists to support control agencies in reducing the sale of forest products obtained illegally. However, this tool still shows only modest results in fulfilling its objectives, since gaps in the system allow illegal wood to be acquired and enter the system as legal wood. The objective of this study was to test whether the volumetric yield coefficient (CRV) of a sawmill on an industrial scale corresponds to the 35% established by Brazilian legislation. The focus was directed at a loophole that allows the accumulation of virtual credits in the DOF system by turning logs into lumber. For this purpose, we estimated the sawmill’s CRV and mean percentage yield of 19 commercial species used by a timber company in the Brazilian Amazon with a sample size of 90 logs. The estimated CRV was 24.6 ± 2.4, showing 9.9% uncertainty. The mean CRV differed highly significantly (p < 0.001) from that proposed by the DOF, with a 10.35% difference. Based on these results, the difference between the observed yield and that proposed by the legislation can generate the accumulation of virtual log credits. With this accumulation, managers encounter difficulties in acquiring new logging permits and, consequently, do not meet the actual demand for logs to the sawmill’s capacity.

VloGraph: A Virtual Knowledge Graph Framework for Distributed Security Log Analysis

The integration of heterogeneous and weakly linked log data poses a major challenge in many log-analytic applications. Knowledge graphs (KGs) can facilitate such integration by providing a versatile representation that can interlink objects of interest and enrich log events with background knowledge. Furthermore, graph-pattern based query languages, such as SPARQL, can support rich log analyses by leveraging semantic relationships between objects in heterogeneous log streams. Constructing, materializing, and maintaining centralized log knowledge graphs, however, poses significant challenges. To tackle this issue, we propose VloGraph—a distributed and virtualized alternative to centralized log knowledge graph construction. The proposed approach does not involve any a priori parsing, aggregation, and processing of log data, but dynamically constructs a virtual log KG from heterogeneous raw log sources across multiple hosts. To explore the feasibility of this approach, we developed a prototype and demonstrate its applicability to three scenarios. Furthermore, we evaluate the approach in various experimental settings with multiple heterogeneous log sources and machines; the encouraging results from this evaluation suggest that the approach can enable efficient graph-based ad-hoc log analyses in federated settings.

Highly Hydrophilic and Lipophilic Derivatives of Bile Salts.

Lipophilicity of 15 derivatives of sodium cholate, defined by the octan-1-ol/water partition coefficient (log P), has been theoretically determined by the Virtual log P method. These derivatives bear highly hydrophobic or highly hydrophilic substituents at the C3 position of the steroid nucleus, being linked to it through an amide bond. The difference between the maximum value of log P and the minimum one is enlarged to 3.5. The partition coefficient and the critical micelle concentration (cmc) are tightly related by a double-logarithm relationship (), meaning that the Gibbs free energies for the transfer of a bile anion from water to either a micelle or to octan-1-ol differ by a constant. The equation also means that cmc can be used as a measurement of lipophilicity. The demicellization of the aggregates formed by three derivatives of sodium cholate bearing bulky hydrophobic substituents has been studied by surface tension and isothermal titration calorimetry. Aggregation numbers, enthalpies, free energies, entropies, and heat capacities, ΔCP,demic, were obtained. ΔCP,demic, being positive, means that the interior of the aggregates is hydrophobic.

Abstract No. 517 Virtual follow-up of percutaneous drains placed in interventional radiology during the COVID-19 pandemic

Evaluate a virtual platform to track percutaneous drains in real-time to guide IR drain management during phase I (pre-resurgence) and II (resurgence) of the COVID-19 pandemic. A prospective review of all patients undergoing percutaneous drain placement in IR between March and August 2020 was carried out (n = 98). All patients undergoing percutaneous drainage of a fluid collection with eventual discharge to home were included. Those with indwelling tubes at the end of the study period were excluded (n = 20). A total of 78 drains met inclusion criteria. Patients were instructed on how to utilize the virtual log, which included daily drain outputs, presence/absence of leakage (spontaneous or with flushing), and daily body temperature prior to discharge. This virtual log was accessed by patients through the patient portal via a computer or smart phone and was integrated into the electronic medical record for provider review. A Fisher’s exact test was used to compare percent compliance during phase I and phase II. Unpaired two-tailed t-tests were used to compare mean time to tube removal (mTTR). Compliance with virtual drain log usage was 30.8% [24/78] with no significant difference between phase I and II (P > 0.05). mTTR ± SE was 44.7 ± 7.1 days in patients who did not use the virtual log, compared with 36.9 ± 8.2 days in patients who did use the virtual log with a difference of 7.8 days, which did not reach statistical significance (P > 0.05). There was a statistically significant difference of 30.6 days in overall mTTR between phase I and phase II (P = 0.007) with a significant difference of 34.5 days between phase I and phase II in the sub-group that did not use the virtual drain log (P = 0.018). There was no significant difference between phase I and phase II in the group that used the virtual drain log. This study demonstrates a significantly increased mTTR in patients who did not use a virtual drain log during the most restrictive phase of the COVID-19 pandemic. Virtual platforms to guide clinical decision making are important tools in health care delivery, particularly with increasing utilization of telehealth services.

Experimental Lipophilicity for Beyond Rule of 5 Compounds

Aim: To set up a chromatographic strategy for the determination of log P for beyond Rule of 5 (bRo5) drugs. Materials & methods: Capacity factors measured by reverse phase-HPLC. Balance of intermolecular interactions governing systems assessed by partial least squares regression (PLSR) coupled with block relevance anaysis (PLSR-BR) and multiblock PLSR (MBPLSR). Determination of virtual log P obtained through conformational sampling. Results: log k′60 is highly correlated with log P for a dataset of 36 Ro5 compliant compounds (R2 = 0.93, Q2 = 0.90). We refer to the value generated via this method as BRlogP. The balance of intermolecular forces controlling BRlogP and log P are very similar. The ElogPs measured for the bRo5 dataset are significantly higher than corresponding BRlogP. Conclusion: The combination of BRlogP and ElogP provides an experimental lipophilicity range for bRo5 compounds.

Official Maps and Everyday Life Cartography: Tensions Movements of Experiences in Space

Can the world be represented by point, line, and polygon? Are maps the world's mirrors? This paper starts with those questions in order to discuss some ways to study urban space in its complexity. Therefore, we tensioned the concepts of cartography into two aspects: as a discipline, which rules the production of the official maps and as a methodological process for the experience in the city. The first part is based on modern science to produce maps apparently impartial. It hides that maps are generalized representations and reductions of the space complexity. The second part approaches the concepts of cartography and the one of rhizome. The cartography, understood as a methodological process, opens itself to other inputs, combinations, and developments. We call it everyday life cartography, when this process is focused in everyday practices. In addition, we showed that is possible to use websites and applications of geo-visualization and geo-collaboration as virtual log books. This practice is adequate only when considered as a tool and not as a final product. It would be a deviationist tactic, as it appropriates techniques used by the strategy of producing official maps to construct other points of views about the city and to overcome stigmas broadcast by the official maps.

MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design.

The molecular lipophilicity potential (MLP) is a well-established method to calculate and visualize lipophilicity on molecules. We are here introducing a new computational tool named MLP Tools, written in the programming language Python, and conceived as a free plugin for the popular open source molecular viewer PyMOL. The plugin is divided into several sub-programs which allow the visualization of the MLP on molecular surfaces, as well as in three-dimensional space in order to analyze lipophilic properties of binding pockets. The sub-program Log MLP also implements the virtual log P which allows the prediction of the octanol/water partition coefficients on multiple three-dimensional conformations of the same molecule. An implementation on the recently introduced MLP GOLD procedure, improving the GOLD docking performance in hydrophobic pockets, is also part of the plugin. In this article, all functions of the MLP Tools will be described through a few chosen examples.

Predicting the physicochemical profile of diastereoisomeric histidine‐containing dipeptides by property space analysis

This study aimed at measuring the lipophilicity and ionization constants of diastereoisomeric dipeptides, interpreting them in terms of conformational behavior, and developing statistical models to predict them. A series of 20 dipeptides of general structure NH(2)-L-X-(L or D)-His-OMe was designed and synthetized. Their experimental ionization constants (pK(1), pK(2) and pK(3)) and lipophilicity parameters (log P(N) and log D(7.4)) were measured by potentiometry. Molecular modeling in three media (vacuum, water, and chloroform) was used to explore and sample their conformational space, and for each stored conformer to calculate their radius of gyration, virtual log P (preferably written as log P(MLP), meaning obtained by the molecular lipophilicity potential (MLP) method) and polar surface area (PSA). Means and ranges were calculated for these properties, as was their sensitivity (i.e., the ratio between property range and number of rotatable bonds). Marked differences between diastereoisomers were seen in their experimental ionization constants and lipophilicity parameters. These differences are explained by molecular flexibility, configuration-dependent differences in intramolecular interactions, and accessibility of functional groups. Multiple linear equations correlated experimental lipophilicity parameters and ionization constants with PSA range and other calculated parameters. This study documents the differences in lipophilicity and ionization constants between diastereoisomeric dipeptides. Such configuration-dependent differences are shown to depend markedly on differences in conformational behavior and to be amenable to multiple linear regression.

Molecular Interaction Fields (MIFs) to Predict Lipophilicity and ADME Profile of Antitumor Pt(II) Complexes

To describe a computational tool to calculate molecular descriptors of potential application in ADME virtual screening of antitumor Pt(II) drug candidates. The multistep computational procedure consists in (a) building and optimization (PM3) of the 3D structures of the investigated complexes, (b) parametrization of Pt(II) and its implementation in GRID, (c) GRID calculations and extraction of the information content with VolSurf and BIOCUBE4mf, and (d) PLS analysis to look for the correlation between experimental data and the molecular descriptors. The following results were obtained: (a) the calibration of the GRID force field to take into account the platinum di-cation, (b) solid PLS models between log k30 and log kw with VolSurf descriptors which highlight the main structural differences between the two chromatographic parameters, (c) the prediction of virtual (of each conformer) log k30 and log kw, and (d) the identification of the main descriptors governing VD(ss) of drugs in clinical use. The study suggests a strategy to identify good Pt(II) complexes prior to their synthesis to eliminate as soon as possible drug candidates with unfavorable PK profile.

Partition Coefficient and Molecular Flexibility: The Concept of Lipophilicity Space

The rationale of this study was to investigate molecular flexibility and its influence on physicochemical properties with a view to uncovering additional information on the fuzzy concept of dynamic molecular structure. Indeed, it is now known that computed molecular interaction fields (MIFs) such as molecular electrostatic potentials (MEPs) and lipophilicity potentials (MLPs) are conformation-dependent, as are dipole moments. A database of 125 compounds was used whose conformational space was explored, while conformation-dependent parameters were computed for each non-redundant conformer found in the conformational space of the compounds. These parameters were the virtual log P (log P(MLP), calculated by a MLP approach), the apolar surface area (ASA), polar surface area (PSA), and solvent-accessible surface (SAS). For each compound, the range taken by each parameter (its property space) was divided by the number of rotors taken as an index of flexibility, yielding a parameter termed 'molecular sensitivity'. This parameter was poorly correlated with others (i.e., it contains novel information) and showed the compounds to fall into two broad classes. 'Sensitive' molecules are those whose computed property ranges are markedly sensitive to conformational effects, whereas 'insensitive' (in fact, less sensitive) molecules have property ranges which are comparatively less affected by conformational fluctuations. A pharmacokinetic application is presented.

A QSAR study of acute toxicity of N-substituted fluoroacetamides to rats

Acute toxicity in vivo toward rats, of nineteen N-alkyl and N-cycloalkyl fluorocetamides [F–CH 2–C(O)–NH–R] was correlated with their structure-dependent properties. Used descriptors are: molecular weights ( M w) and heat of formation (Δ H f) of compounds; molar refractivity (CMR), lipophilicity (Clog P), Broto lipol values, virtual log P, molecular lipophilic potential (MLP), Van der Waals surfaces (VdW SAS) and hydropathicity surface (ILM) of whole molecules; Taft steric parameters ( E s); E s values with Hancock corrections ( E s CH ) and Verloop sterimol ( B 5) and ( L) parameters of alkyl and cycloalkyl residues; superdelocalizabilities and electron densities on the [NH–C(O)–CH 2–F] fragment. Strong quantitative structure–activity relationships were assessed. Obtained correlation suggested that lipophilicity, shape and bulkiness of the alkyl and cycloalkyl substituents, particular nearest vicinity of the amide nitrogen, as well charges on the amide moiety are the main factors that influence on the acute toxicity of studied compounds toward rats. Mechanism of toxic action was proposed.

Calculating Virtual log Pin the Alkane/Water System (log PNalk) and Its Derived Parameters Δlog PNoct-alkand log DpHalk

Growing interest in the use of both the logarithm of the partition coefficient of the neutral species in the alkane/water system (log P(N)(alk)) and the difference between log P(N)(oct) (the logarithm of the partition coefficient of the neutral species in the n-octanol/water system) and log P(N)(alk) (Deltalog P(N)(oct-alk)) in the early stages of drug design has stimulated development of a computational tool based on the Volsurf software to predict virtual (=of each conformer) log P(N)(alk) and virtual log P(N)(oct). From these two pieces of data, it is then possible to calculate Deltalog P(N)(oct-alk) for a given compound as the difference between log P(N)(oct) and log P(N)(alk). Once the pK(a) is known and the legitimacy of neglecting the contribution made by the ionized species has been checked, it is also possible to calculate log D(pH)(alk), which might be an important lipophilicity descriptor in absorption, distribution, metabolism, and excretion (ADME) prediction, from log P(N)(alk).

Solvent Constraints on the Property Space of Acetylcholine. I. Isotropic Solvents

The objective of this study was, first, to examine the property space of a test molecule and, second, to assess solvent constraints. Acetylcholine was chosen as the object of study given its interesting molecular structure and major biological significance. Molecular dynamics simulations of long duration (30 ns) were carried out with acetylcholine in a vacuum or in a box of solvent (chloroform, water, water plus one chloride counterion). For each of the 6000 conformers stored during each run, various geometric and physicochemical properties were calculated, namely, N(+)-C8 distance, solvent-accessible surface area (SAS), polar surface area (PSA), dipole moment, and lipophilicity (virtual log P). The variations of these properties as a function of the dihedral angles tau(2) and tau(3) were unexpectedly broad for such a small molecule. Dipole moment and virtual log P were well correlated, and they varied in a complex manner with the dihedral angles. For example, each of the seven conformational clusters was able to access much of the lipophilicity space of acetylcholine. Solvent constraints on the property space clearly indicate that a polar medium tends to favor polar conformers, whereas the opposite is true for a solvent of low polarity.

La probabilité d'hydratation moléculaire : un nouveau concept pour le calcul du log P dune molécule à partir de sa structure 3D (text in French)

A new concept, the Moleculer Hydration Probability (MHP), depending on the 3D structure of a molecule and on the composition of the first hydration shell, is presented. The knowledge of MHP allows the estimation of virtual log P on the van der Waals surface of molecules.

Structure–Property Relationships of Trimetazidine Derivatives and Model Compounds as Potential Antioxidants

Twenty-five compounds (trimetazidine derivatives and other compounds, mostly having a free phenolic group) were examined for their radical scavenging and antioxidant properties. Their reaction with DPPH (2,2-diphenyl-1-picrylhydrazyl) as a measure of radical scavenging capacity was assessed by two parameters, namely EC 50 (the concentration of antioxidant decreasing DPPH by 50%), and log Z, a kinetic parameter proposed here and derived from initial second-order rate constants and antioxidant/DPPH ratios. Antioxidant activities were determined by the inhibition of lipid peroxidation and albumin oxidation. The most active compounds were derivatives having a trolox or hydroquinone moiety. Physicochemical and structural properties were determined by molecular modeling as lipophilicity (virtual log P calculations) and H-Surf (solvent-accessible surface of hydroxyl hydrogen) and by quantum mechanical calculations (ΔH ox = oxidation enthalpy; ΔH abs = enthalpy of hydrogen abstraction). QSAR models were derived to identify molecular mechanisms responsible for the reactivity toward the DPPH radical and for the inhibition of lipid peroxidation. A useful prediction of antioxidant capacity could be achieved from calculated molecular properties and the kinetic parameter developed here.