A fast and efficient algorithm for DNA sequence similarity identification.

DNA sequence similarity analysis is necessary for enormous purposes including genome analysis, extracting biological information, finding the evolutionary relationship of species. There are two types of sequence analysis which are alignment-based (AB) and alignment-free (AF). AB is effective for small homologous sequences but becomes NP-hard problem for long sequences. However, AF algorithms can solve the major limitations of AB. But most of the existing AF methods show high time complexity and memory consumption, less precision, and less performance on benchmark datasets. To minimize these limitations, we develop an AF algorithm using a 2D k - m e r count matrix inspired by the CGR approach. Then we shrink the matrix by analyzing the neighbors and then measure similarities using the best combinations of pairwise distance (PD) and phylogenetic tree methods. We also dynamically choose the value of k for k - m e r . We develop an efficient system for finding the positions of k - m e r in the count matrix. We apply our system in six different datasets. We achieve the top rank for two benchmark datasets from AFproject, 100% accuracy for two datasets (16 S Ribosomal, 18 Eutherian), and achieve a milestone for time complexity and memory consumption in comparison to the existing study datasets (HEV, HIV-1). Therefore, the comparative results of the benchmark datasets and existing studies demonstrate that our method is highly effective, efficient, and accurate. Thus, our method can be used with the top level of authenticity for DNA sequence similarity measurement.

Pseudotetrahedral Zn(II)-(R or S)-dihalogen-salicylaldiminato complexes with Λ- or Δ-chirality induction at-metal.

Reactions of enantiopure (S or R)-N-1-(phenyl)ethyl-2,4-X1,X2-salicylaldimine (S-H or R-H; X1, X2 = dihalogen) with Zn(II)-nitrate give bis[(S or R)-N-1-(phenyl)ethyl-2,4-X1,X2-salicylaldiminato-κ2N,O]-zinc(II), (Δ-ZnS or Λ-ZnR) with Δ/Λ-chirality induction at-metal in the C2-symmetric molecules. EI-mass spectra show parent ion peaks. X-ray structures indicate that two phenolate-oxygen and two imine-nitrogen atoms from two molecules of the Schiff bases coordinate to the Zn(II) ion in a pseudotetrahedral geometry. Structural analyses give evidence that the S- or R-ligand chirality gives only one diastereomer Δ-ZnS or Λ-ZnR in an enantiopure crystal. Gas-phase optimized structures suggest that the Δ-ZnS or Λ-ZnR diastereomers are slightly more stable than Λ-ZnS or Δ-ZnR by 1-2 kcal mol-1. The intramolecular interactions were analyzed with the Independent Gradient Model (IGM) using the program Multiwfn on the optimized structures and also indicate the diastereomeric preference of Δ-ZnS1 over Λ-ZnS1 (or Λ-ZnR1 over Δ-ZnR1). Variable time and temperature 1H NMR spectra support the presence of only one diastereomer Λ-ZnR or Δ-ZnS in the bulk samples, backed by the simulated spectra which exhibit no diastereomerization in solution. In contrast, the reported Zn(II)-(R or S)-salicylaldiminato/naphthaldiminato complexes show a diastereomeric mixture of both Δ- and Λ-forms and a Δ â‡„ Λ equilibrium in solution. Electronic circular dichroism (ECD) spectra in solution display expected mirror-image relationships for the (S or R)-Schiff base ligands and the (S or R)-ligated complexes. Combined analyses of experimental and simulated ECD spectra further support the notion of diastereomeric excess of Δ-ZnS or Λ-ZnR in solution. The overall results thus suggest the preservation of chirality at-zinc induced by S- or R-ligands in a solid or solution. Supramolecular packing analyses explore different kinds of intermolecular interactions with the strongest one for X⋯O. Only the halogen atom in the para position is involved in these interactions with Br⋯O > Cl⋯O. Hirshfeld surface analyses also support these interactions between two molecules at a distance shorter than the sum of the vdW radii. Comparison of the experimental and simulated PXRD patterns from the single-crystal X-ray structures shows a good matching and confirms the phase purity of the bulk samples.

Synthesis and Characterization of Bis[(R or S)-N-1-(X-C6H4)ethyl-2-oxo-1-naphthaldiminato-κ2N,O]-Λ/Δ-cobalt(II) (X = H, p-CH3O, p-Br) with Symmetry- and Distance-Dependent Vibrational Circular Dichroism Enhancement and Sign Inversion.

The enantiopure Schiff bases (R or S)-N-1-(X-C6H4)ethyl-2-hydroxy-1-naphthaldimine {X = H [(R or S)-HL1], p-CH3O [(R or S)-HL2], and p-Br [(R- or S)-HL3]} react with cobalt(II) acetate to give bis[(R or S)-N-1-(X-C6H4)ethyl-2-oxo-1-naphthaldiminato-κ2N,O]-Λ/Δ-cobalt(II) {X = H [Λ/Δ-Co-(R or S)-L1], p-CH3O [Λ/Δ-Co-(R or S)-L2], and p-Br [Λ/Δ-Co-(R or S)-L3]} (1-3), respectively. Induced Λ and Δ chirality originates at the metal center of the C2-symmetric molecule in pseudotetrahedral geometry. Differential scanning calorimetry analyses explored the thermal stability of the complexes, which undergo reversible phase transformation from crystalline solid to isotropic liquid phase for 1 and 3 but irreversible phase transformation for 2. Like other cobalt(II) complexes, compounds 1-3 exhibit a continuous ensemble of absorption and circular dichroism bands, which span from the UV to IR region and can be collected into a superspectrum. Infrared vibrational circular dichroism (IR-VCD) spectra witness the coupling between Co2+-centered low-lying electronic states and ligand-centered vibrations. The coupling produces enhanced and almost monosignate VCD spectra, with both effects being mode-dependent in terms of the A or B symmetry (in the C2 point group) and distance from the Co2+ core.

Pseudotetrahedral copper(II)-complexes with enantiopure (R or S)-2-(((aryl)ethylimino)ethyl)phenolate Schiff base ligands.

Condensation of 2-hydroxy-benzophenone (HL') with (R or S)-(Ar)ethylamine yields the enantiopure Schiff bases (S or R)-2-((E)-1-(1-(Ar)ethylimino)ethyl)phenol {Ar = C6H5 (S- or R-HL1), p-CH3OC6H4 (S- or R-HL2)}. These Schiff bases react with copper(ii) acetate under reflux to give green microcrystals of bis[(R or S)-2-((E)-1-(1-(Ar)ethylimino)ethyl)phenolato-κ2N,O]-Λ/Δ-copper(ii), {Ar = C6H5 (Λ/Δ-Cu-R- or S-L1), p-CH3OC6H4 (Λ/Δ-Cu-R- or S-L2)} with induction of Λ/Δ-chirality at-metal. The presence of Schiff base ligands in the paramagnetic green microcrystals is confirmed by decomplexation reaction with NaCN via reduction of Cu(ii) to Cu(i) in DMSO-d6 solution. Crystallization attempts of the green microcrystalline Schiff-base Cu complexes provide deep-green block-shaped crystals of an about equal admixture of bis[2-oxo-benzophenonato-κ2O,O']-copper(ii), (CuL'2) and bis[2-(imino(phenyl)methyl)phenolato-κ2N,O]copper(ii), (CuL''2) via in situ hydrolysis of the coordinated Schiff base ligands back to 2-hydroxy-benzophenone (HL') and to 2-(imino(phenyl)methyl)phenol (HL''), which in-turn bind with the copper(ii) ion. Powder X-ray diffraction (PXRD) patterns of R-HL1 and Cu-R-L1 allowed their structure determinations using the program Expo-2014 followed by Rietveld refinement. The Cu structures refined to four-coordinated Λ/Δ-copper(ii)-complexes by the two phenolate-oxygen and two imine-nitrogen atoms from two Schiff base ligands in a pseudotetrahedral geometry. DFT optimized structures (at gas-phase) reveal the Δ-Cu-S-L1 or Λ-Cu-R-L1 diastereomer as slightly more stable than the corresponding Λ-Cu-S-L1 or Δ-Cu-R-L1 by ca. 7.60 kcal mol-1, resulting from diastereoselectively induced Λ vs. Δ-chirality at-metal. Electronic circular dichroism (ECD) spectra display mirror-image relationships and comparisons of experimental and simulated ECD spectra by TDDFT suggest an excess of the Δ-Cu-S-L1 or Λ-Cu-R-L1 diastereomer in solution. The cyclic voltammograms demonstrate two one electron charge transfer processes for Cu2+/Cu+ and Cu+/Cu0 couples in acetonitrile, respectively.

4P Model for Dynamic Prediction of COVID-19: a Statistical and Machine Learning Approach.

Around the world, scientists are racing hard to understand how the COVID-19 epidemic is spreading and growing, thus trying to find ways to prevent it before medications are available. Many different models have been proposed so far correlating different factors. Some of them are too localized to indicate a general trend of the pandemic while some others have established transient correlations only. Hence, in this study, taking Bangladesh as a case, a 4P model has been proposed based on four probabilities (4P) which have been found to be true for all affected countries. Efficiency scores have been estimated from survey analysis not only for governing authorities on managing the situation (P(G)) but also for the compliance of the citizens ((P(P)). Since immune responses to a specific pathogen can vary from person to person, the probability of a person getting infected ((P(I)) after being exposed has also been estimated. And the vital one is the probability of test positivity ((P(T)) which is a strong indicator of how effectively the infected people are diagnosed and isolated from the rest of the group that affects the rate of growth. All the four parameters have been fitted in a non-linear exponential model that partly updates itself periodically with everyday facts. Along with the model, all the four probabilistic parameters are engaged to train a recurrent neural network using long short-term memory neural network and the followed trial confirmed a ruling functionality of the 4Ps.