Yeast cell detection using fuzzy automatic contrast enhancement (FACE) and you only look once (YOLO).

In contemporary biomedical research, the accurate automatic detection of cells within intricate microscopic imagery stands as a cornerstone for scientific advancement. Leveraging state-of-the-art deep learning techniques, this study introduces a novel amalgamation of Fuzzy Automatic Contrast Enhancement (FACE) and the You Only Look Once (YOLO) framework to address this critical challenge of automatic cell detection. Yeast cells, representing a vital component of the fungi family, hold profound significance in elucidating the intricacies of eukaryotic cells and human biology. The proposed methodology introduces a paradigm shift in cell detection by optimizing image contrast through optimal fuzzy clustering within the FACE approach. This advancement mitigates the shortcomings of conventional contrast enhancement techniques, minimizing artifacts and suboptimal outcomes. Further enhancing contrast, a universal contrast enhancement variable is ingeniously introduced, enriching image clarity with automatic precision. Experimental validation encompasses a diverse range of yeast cell images subjected to rigorous quantitative assessment via Root-Mean-Square Contrast and Root-Mean-Square Deviation (RMSD). Comparative analyses against conventional enhancement methods showcase the superior performance of the FACE-enhanced images. Notably, the integration of the innovative You Only Look Once (YOLOv5) facilitates automatic cell detection within a finely partitioned grid system. This leads to the development of two models-one operating on pristine raw images, the other harnessing the enriched landscape of FACE-enhanced imagery. Strikingly, the FACE enhancement achieves exceptional accuracy in automatic yeast cell detection by YOLOv5 across both raw and enhanced images. Comprehensive performance evaluations encompassing tenfold accuracy assessments and confidence scoring substantiate the robustness of the FACE-YOLO model. Notably, the integration of FACE-enhanced images serves as a catalyst, significantly elevating the performance of YOLOv5 detection. Complementing these efforts, OpenCV lends computational acumen to delineate precise yeast cell contours and coordinates, augmenting the precision of cell detection.

Polyphenols bind to low density lipoprotein at biologically relevant concentrations that are protective for heart disease.

There is ample evidence in the epidemiological literature that polyphenols, the major non-vitamin antioxidants in plant foods and beverages, have a beneficial effect on heart disease. Until recently other mechanisms which polyphenols exhibit such as cell signaling and regulating nitric oxide bioavailability have been investigated. The oxidation theory of atherosclerosis implicates LDL oxidation as the beginning step in this process. Nine polyphenols from eight different classes and several of their O-methylether, O-glucuronide and O-sulfate metabolites have been shown in this study to bind to the lipoproteins and protect them from oxidation at lysosomal/inflammatory pH (5.2), and physiological pH (7.4). Polyphenols bind to the apoprotein at pH 7.4 with Kb > 106 M-1 and the number of molecules of polyphenols bound per LDL particle under saturation conditions varied from 0.4 for ferulic acid to 13.1 for quercetin. Competition studies between serum albumin and LDL show that substantial lipoprotein binding occurs even in the presence of a great molar excess of albumin, the major blood protein. These in vitro results are borne out by published human supplementation studies showing that polyphenol metabolites from red wine, olive oil and coffee are found in LDL even after an overnight fast. A single human supplementation with various fruit juices, coffee and tea also produced an ex vivo protection against lipoprotein oxidation under postprandial conditions. This in vivo binding is heart-protective based on published olive oil consumption studies. Relevant to heart disease, we hypothesize that the binding of polyphenols and metabolites to LDL functions as a transport mechanism to carry these antioxidants to the arterial intima, and into endothelial cells and macrophages. Extracellular and intracellular polyphenols and their metabolites are heart-protective by many mechanisms and can also function as potent "intraparticle" and intracellular antioxidants due to their localized concentrations that can reach as high as the micromolar level. Low plasma concentrations make polyphenols and their metabolites poor plasma antioxidants but their concentration in particles such as lipoproteins and cells is high enough for polyphenols to provide cardiovascular protection by direct antioxidant effects and by other mechanisms such as cell signaling.

Self-assembling of peptides is tuned via an extended amphipathic helix.

Four peptides, C1 (spanning the helical segment of human neuropeptide Y from residue 15 to residue 29), C2 (spanning the helical segment of 21 to 31), C3 (the C-terminal fragment of neuropeptide Y involving residues 20 to 36) and P34-C3 (replacement of the glutamine with proline in position 34 of C3) were synthesized to study interaction between species. The information about the intermolecular interactions was extracted from their self-assembly behaviors. The results from CD and NMR showed that the addition of 2,2,2-trifluoroethanol (TFE) induces a stable amphipathic helix in each peptides and an extended helix was formed at the N-terminal of C1 and the C-terminal of C3. Pulsed field gradient NMR data revealed that C3 may undergo an enhanced interaction with TFE and a more favorable self-assembly as temperature was increased. In contrast, other three peptides were found to form larger size of oligomers at lower temperature and continuously dissociate into the monomeric form with increased temperature. Our results demonstrate that the self-assembly behavior may be tuned by the entropy and the energetics contributed by an extended helical conformation at terminus.

Accurate potential energy curve of the LiH+ molecule calculated with explicitly correlated Gaussian functions.

Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

Deletion of the carboxyl-terminal residue disrupts the amino-terminal folding, self-association, and thermal stability of an amphipathic antimicrobial peptide.

Understanding the complex relationship between amino acid sequence and protein behaviors, such as folding and self-association, is a major goal of protein research. In the present work, we examined the effects of deleting a C-terminal residue on the intrinsic properties of an amphapathic α-helix of mastoparan-B (MP-B), an antimicrobial peptide with the sequence LKLKSIVSWAKKVL-NH2. We used circular dichroism and nuclear magnetic resonance to demonstrate that the peptide MP-B([1-13]) displayed significant unwinding at the N-terminal helix compared with the parent peptide of MP-B, as the temperature increased when the residue at position 14 was deleted. Pulsed-field gradient nuclear magnetic resonance data revealed that MP-B forms a larger diffusion unit than MP-B([1-13]) at all experimental temperatures and continuously dissociates as the temperature increases. In contrast, the size of the diffusion unit of MP-B([1-13]) is almost independent of temperature. These findings suggest that deleting the flexible, hydrophobic amino acid from the C-terminus of MP-B is sufficient to change the intrinsic helical thermal stability and self-association. This effect is most likely because of the modulation of enthalpic interactions and conformational freedom that are specified by this residue. Our results implicate terminal residues in the biological function of an antimicrobial peptide.

Analytical energy gradient used in variational Born-Oppenheimer calculations with all-electron explicitly correlated Gaussian functions for molecules containing one π electron.

An algorithm for variational calculations of molecules with one π electron performed with all-electron explicitly correlated gaussian (ECG) functions with floating centers is derived and implemented. The algorithm includes the analytic gradient of the Born-Oppenheimer electronic energy determined with respect to the ECG exponential parameters and the coordinates of the gaussian centers. The availability of the gradient greatly accelerates the variational energy minimization. The algorithm is tested in calculations of four electronic excited states, c(3)Π(u), C(1)Π(u), i(3)Π(g), and I(1)Π(g), of the hydrogen molecule at a single internuclear distance specific to each state. With the use of the analytical energy gradient, the present calculations yield new, lowest-to-date, variational energy upper bounds for all four states.

Accurate potential energy curves for HeH+ isotopologues.

New accurate ground-state potential energy curves (PEC) for the (4)HeH(+), (4)HeD(+), (3)HeH(+), and (3)HeD(+) isotopologues are calculated with 600 explicitly correlated Gaussian (ECG) functions with shifted centers in the range between R = 0.35 a(0) and 145 a(0). The calculations include the adiabatic corrections (AC). The absolute accuracy of all Born-Oppenheimer (BO) PEC points is better than 0.0018 cm(-1) and it is better than 0.0005 cm(-1) for the ACs. With respect to the very recent BO PEC calculations performed by Pachucki with 20 000 generalized Heitler-London explicitly correlated functions [K. Pachucki, Phys. Rev. A 85, 042511 (2012)], the present energy calculated at R = 1.46 a(0) (a point near the BO equilibrium distance) lies above by only 0.0012 cm(-1). Using Pachucki's BO energy at the equilibrium distance of R = 1.463 283 a(0), and the adiabatic corrections calculated in this work for the (4)HeH(+), (4)HeD(+), (3)HeH(+), and (3)HeD(+) isotopologues, the following values are obtained for their PEC depths: 16 448.99893 cm(-1), 16 456.86246 cm(-1), 16 451.50635 cm(-1), and 16 459.36988 cm(-1), respectively. We also calculate the rovibrational (rovib) frequencies for the four isotopologues using the BO PEC of Pachucki augmented with the present ACs. The improvements over the BO+AC PEC of Bishop and Cheung (BC) [J. Mol. Spectrosc. 75, 462 (1979)] are 1.522 cm(-1) at R = 4.5 a(0) and 0.322 cm(-1) at R = ∞. To partially account for the nonadiabatic effects in the rovib calculations an effective reduced-mass approach is used. With that, the present (4)HeH(+) rovibrational transitions are considerably improved over the BC transitions as compared with the experimental values. Now the rovibrational transitions near the dissociation limit are as well reproduced by the present calculations as the lower transitions. For example, for the (4)HeD(+) transitions corresponding to the ν = 13-9 hot bands the results are off from the experimental values by less than 0.023 cm(-1). This confirms high accuracy of the present PECs at larger internuclear separations.

Very accurate potential energy curve of the He2+ ion.

A very accurate ground-state potential energy curve (PEC) of the He(2)(+) molecule is calculated with 1200 explicitly correlated Gaussian functions with shifted centers in the range between 0.9 and 100 a(0). The calculations include the adiabatic corrections determined for the (3)He(4)He(+), (3)He(2)(+), and (4)He(2)(+) isotopologues. The absolute accuracy of the PEC is better than 0.05 cm(-1) and that of the adiabatic corrections is around 0.01 cm(-1). The depths of the PECs augmented with the adiabatic corrections for the three isotopologues are: 19 956.708 cm(-1) for (4)He(2)(+), 19 957.054 cm(-1) for (3)He(4)He(+), and 19 957.401 cm(-1) for (3)He(2)(+). The rovibrational energies are also determined. For (3)He(4)He(+) the computed rovibrational transitions corresponding to the ν = 1-0 band differ from the experiment by less than 0.005 cm(-1). For the rovibrational transitions corresponding to the ν = 23-22 band the difference is around 0.012 cm(-1). Presently, this represents the best agreement between theory and experiment for He(2)(+).

Characterization the effects of structure and energetics of intermolecular interactions on the oligomerization of peptides in aqueous 2, 2, 2-trifluoroethanol via circular dichroism and nuclear magnetic resonance spectroscopy.

Intermolecular interactions are of fundamental importance to fully comprehend a wide range of protein behaviors such as oligomerization, folding and recognition. Two peptides, NPY([18-36]) and NPY([15-29]), segmented from human neuropeptide Y (hNPY), were synthesized in this work to study the interaction between species. Information about intermolecular interactions was extracted from their oligomerizing behaviors. The results from CD and NMR showed that the addition of 2, 2, 2-trifluoroethanol (TFE) induces a stable helix in each peptides and an extended helix in NPY([18-36]), formed between residues 30-36. Pulsed field gradient NMR data revealed that NPY([15-29]) forms a larger oligomer at lower temperatures and continuously dissociates into the monomeric form with increasing temperature. NPY([18-36]) was also found to undergo an enhanced interaction with TFE and a more favorable self-association at higher temperatures. We characterized the changes of oligomerized states with respect to temperature to infer the effects of entropy and interaction energy on the association-dissociation equilibrium. As shown by NPY([15-29]), deletion of helical secondary structure or residues from the C-terminal segment may disrupt the solvation by TFE and results in entropy increase as the oligomer dissociates. Unlike that in NPY([15-29]), the extended helix in NPY([18-36]) improves the binding of TFE, and as a result, entropy is gained via the transfer of the TFE cluster from the interface between monomeric peptides into the bulk solvent. This observation suggests that the oligomerized state may be modulated by the entropy and energetics contributed by helical segments in the oligomerization process.

Very accurate potential energy curve of the LiH molecule.

We present very accurate calculations of the ground-state potential energy curve (PEC) of the LiH molecule performed with all-electron explicitly correlated Gaussian functions with shifted centers. The PEC is generated with the variational method involving simultaneous optimization of all Gaussians with an approach employing the analytical first derivatives of the energy with respect to the Gaussian nonlinear parameters (i.e., the exponents and the coordinates of the shifts). The LiH internuclear distance is varied between 1.8 and 40 bohrs. The absolute accuracy of the generated PEC is estimated as not exceeding 0.3 cm(-1). The adiabatic corrections for the four LiH isotopologues, i.e., (7)LiH, (6)LiH, (7)LiD, and (6)LiD, are also calculated and added to the LiH PEC. The aforementioned PECs are then used to calculate the vibrational energies for these systems. The maximum difference between the computed and the experimental vibrational transitions is smaller than 0.9 cm(-1). The contribution of the adiabatic correction to the dissociation energy of (7)LiH molecule is 10.7 cm(-1). The magnitude of this correction shows its importance in calculating the LiH spectroscopic constants. As the estimated contribution of the nonadiabatic and relativistic effects to the ground state dissociation energy is around 0.3 cm(-1), their inclusion in the LiH PEC calculation seems to be the next most important contribution to evaluate in order to improve the accuracy achieved in this work.

Accurate one-dimensional potential energy curve of the linear (H2)2 cluster.

We present a sub-0.3 K accuracy, ground-state one-dimensional potential energy curve of the metastable linear configuration of the (H(2))(2) cluster calculated exclusively with explicitly correlated Gaussian functions with shifted centers. The H(2) internuclear distance is kept at the isolated H(2) vibrational ground-state average value of 1.448 736 bohr and the intermonomer separation is varied between 2 and 100 bohrs. The analytical gradient of the energy with respect to the nonlinear parameters of the Gaussians (i.e., the exponents and the coordinates of the shifts) has been employed in the variational optimization of the wave function. Procedures for enlarging the basis set and for adjusting the centers of the Gaussians to the varying intermonomer separation have been developed and used in the calculations.

How to calculate H3 better.

Efficient optimization of the basis set is key to achieving a very high accuracy in variational calculations of molecular systems employing basis functions that are explicitly dependent on the interelectron distances. In this work we present a method for a systematic enlargement of basis sets of explicitly correlated functions based on the iterative-complement-interaction approach developed by Nakatsuji [Phys. Rev. Lett. 93, 030403 (2004)]. We illustrate the performance of the method in the variational calculations of H(3) where we use explicitly correlated Gaussian functions with shifted centers. The total variational energy (-1.674 547 421 Hartree) and the binding energy (-15.74 cm(-1)) obtained in the calculation with 1000 Gaussians are the most accurate results to date.

New more accurate calculations of the ground state potential energy surface of H(3) (+).

Explicitly correlated Gaussian functions with floating centers have been employed to recalculate the ground state potential energy surface (PES) of the H(3) (+) ion with much higher accuracy than it was done before. The nonlinear parameters of the Gaussians (i.e., the exponents and the centers) have been variationally optimized with a procedure employing the analytical gradient of the energy with respect to these parameters. The basis sets for calculating new PES points were guessed from the points already calculated. This allowed us to considerably speed up the calculations and achieve very high accuracy of the results.