*Faraday Discuss ; 221(0): 379-405, 2019 Dec 16.*

**| MEDLINE**| ID: mdl-31591627

##### RESUMO

We present two methods that address the computational complexities arising in hydrogen transfer reactions in enzyme active sites. To address the challenge of reactive rare events, we begin with an ab initio molecular dynamics adaptation of the Caldeira-Leggett system-bath Hamiltonian and apply this approach to the study of the hydrogen transfer rate-determining step in soybean lipoxygenase-1. Through direct application of this method to compute an ensemble of classical trajectories, we discuss the critical role of isoleucine-839 in modulating the primary hydrogen transfer event in SLO-1. Notably, the formation of the hydrogen bond between isoleucine-839 and the acceptor-OH group regulates the electronegativity of the donor and acceptor groups to affect the hydrogen transfer process. Curtailing the formation of this hydrogen bond adversely affects the probability of hydrogen transfer. The second part of this paper deals with complementing the rare event sampled reaction pathways obtained from the aforementioned development through quantum nuclear wavepacket dynamics. Essentially the idea is to construct quantum nuclear dynamics on the potential surfaces obtained along the biased trajectories created as noted above. Here, while we are able to obtain critical insights on the quantum nuclear effects from wavepacket dynamics, we primarily engage in providing an improved computational approach for efficient representation of quantum dynamics data such as potential surfaces and transmission probabilities using tensor networks. We find that utilizing tensor networks yields an accurate and efficient description of time-dependent wavepackets, reduced dimensional nuclear eigenstates and associated potential energy surfaces at much reduced cost.

*J Chem Theory Comput ; 15(11): 5769-5786, 2019 Nov 12.*

**| MEDLINE**| ID: mdl-31557011

##### RESUMO

We present a new approach for adaptive molecular fragmentation. Here multiple fragmentation protocols, or fragmentation topologies, are combined to efficiently and accurately construct potential energy surfaces that are in agreement with post-Hartree-Fock levels of electronic structure theories at density functional theory (DFT) cost. We benchmark the method through evaluation of quantum nuclear effects in a set of protonated water clusters that are known to display significant quantum effects. In such systems, the straightforward use of molecular fragmentation is hindered by the fact that the most appropriate fragmentation strategy changes as a function of nuclear degrees of freedom. Our approach uses a multilayered hypergraph formalism to decompose the potential energy surface, where, at the very top layer, a tessellation of the potential surface yields a set of independent, but correlated, graphical nodes or vertices; each node represents a different protocol to fragment the molecular system. Correlation between the nodes appears as edges and faces in the graph at the top layer and allows the overall potential surface to be represented as a superposition of multiple fragmentation topologies with the coefficients for the superposition arising from a Hamiltonian formalism that is reminiscent of nonadiabatic dynamics. This allows for a natural interpretation of the individual molecular fragmentation topologies as diabatic or valence-bond-type states which we exploit in our formalism. As stated, the method is demonstrated for protonated water clusters where we are able to obtain potentials surfaces in agreement with post-Hartree-Fock methods at DFT cost.

*Indian J Med Ethics ; 4(2): 115-120, 2019.*

**| MEDLINE**| ID: mdl-31271363

##### RESUMO

This paper primarily discusses the judgment of the Delhi High Court on the government's ban on the use of Oxytocin. Part 1 recapitulates the events leading up to the ban and Part 2 discusses the legal issues considered by the Court before pronouncing its judgment. The paper outlines how life and death issues caused by the ban on a drug have finally been settled by legal considerations, apparently obscure to the non-specialist, but necessary to be understood by health policy makers.

*Indian J Anaesth ; 63(6): 462-468, 2019 Jun.*

**| MEDLINE**| ID: mdl-31263298

##### RESUMO

Background and Aims: Epidural analgesia (EA) and transversus abdominal plane (TAP) block have been part of multimodal analgesia techniques for postoperative pain relief in abdominal surgeries though EA has been established as gold standard. This study assesses and compares the analgesic efficacy of continuous bilateral TAP catheter infusion and lumbar epidural infusion. Methods: In this randomised, single-blind, prospective, non-inferiority trial, 75 patients were randomised to receive a bolus dose of 15 ml, 0.25% bupivacaine followed by an infusion of 5-12 ml/h of 0.125% bupivacaine via lumbar epidural in EA group and a bolus dose of 0.4 ml/kg of 0.25% bupivacaine bilaterally via TAP catheter followed by continuous infusion at 5ml/h of 0.125% bupivacaine in TAP group postoperatively. VAS scores (primary objective) and sensory dermatome blockade were recorded at 1, 4, 8, 12 and 24 h. Total morphine consumption, PONV, incidence of hypotension and patient satisfaction scales were recorded at the end of 24 hours. Results: The median VAS scores were comparable between the groups at 1, 4, 8, 12 and 24 hours both at rest (P = 0.11, 0.649, 0.615, 0.280 and 0.191, respectively) and on coughing (p = 0.171, 0.224, 0.207, 0.142 and 0.158, respectively). Total morphine consumption in 24 h between TAP and EA group was comparable (p = 0.366). There was no statistical difference in the incidence of hypotension, PONV and patient satisfaction scale. Conclusion: Continuous bilateral TAP block is as efficacious as the continuous lumbar epidural infusion in relieving postoperative pain in patients undergoing lower abdominal surgeries.

*Dig Dis Sci ; 64(12): 3502-3517, 2019 Dec.*

**| MEDLINE**| ID: mdl-31187328

##### RESUMO

BACKGROUND: Gastrointestinal (GI) motility dysfunction is the most common non-motor symptom of Parkinson's disease (PD). Studies have indicated that GI motility functions are impaired before the onset of PD. AIMS: To investigate the underlying mechanism of PD-induced GI dysmotility in MPTP (1-methyl 4-phenyl 1,2,3,6-tetrahydropyridine)-induced animal model. METHODS: C57BL/6 mice were administered with or without a selective dopamine neurotoxin, MPTP, to induce parkinsonian symptoms. In addition to in vivo studies, in vitro experiments were also conducted in colon specimens using l-methyl-4-phenylpyridinium (MPP+), a metabolic product of MPTP. Gastric emptying, colon motility, nitrergic relaxation, and western blot experiments were performed as reported. RESULTS: MPTP-induced PD mice showed decreased expression of nuclear factor erythroid 2-related factor (Nrf2) and its target phase II genes in gastric and colon neuromuscular tissues. Decreased levels of tetrahydrobiopterin (BH4, a critical cofactor for nNOS dimerization) associated with uncoupling of nNOS in gastric and colon tissues exposed to MPTP. Impaired enteric nitrergic system led to delayed gastric emptying and slower colonic motility compared to the control mice. In vitro results in colon specimens confirm that activation of Nrf2 restored MPP+-induced suppression of alpha-synuclein, tyrosine hydroxylase (TH), Nrf2, and heme oxygenase-1. In vitro exposure to L-NAME [N(w)-nitro-L-arginine methyl ester], a NOS synthase inhibitor, reduced protein expression of TH in colon tissue homogenates. CONCLUSIONS: Loss of Nrf2/BH4/nNOS expression in PD impairs antioxidant gene expression, which deregulates NO synthesis, thereby contributing to the development of GI dysmotility and constipation. Nitric oxide appears to be important to maintain dopamine synthesis in the colon.

*J Chem Theory Comput ; 15(5): 2780-2796, 2019 May 14.*

**| MEDLINE**| ID: mdl-31002502

##### RESUMO

We present an approach to reduce the computational complexity and storage pertaining to quantum nuclear wave functions and potential energy surfaces. The method utilizes tensor networks implemented through sequential singular value decompositions. Two specific forms of tensor networks are considered to adaptively compress the data in multidimensional quantum nuclear wave functions and potential energy surfaces. In one case the well-known matrix product state approximation is used whereas in another case the wave function and potential energy surface space is initially partitioned into "system" and "bath" degrees of freedom through singular value decomposition, following which the individual system and bath tensors (wave functions and potentials) are in turn decomposed as matrix product states. We postulate that this leads to a mean-field version of the well-known projectionally entangled pair state known in the tensor networks community. Both formulations appear as special cases of more general higher order singular value decompositions known in the mathematics literature as Tucker decomposition. The networks are then used to study the hydrogen transfer step in the oxidation of isoprene by peroxy and hydroxy radicals. We find that both networks are extremely efficient in accurately representing quantum nuclear eigenstates and potential energy surfaces and in computing inner products between quantum nuclear eigenstates and a final-state basis to yield product side probabilities. We also present formal protocols that will be useful to perform explicit quantum nuclear dynamics.

*Br J Neurosurg ; 33(2): 125-130, 2019 Apr.*

**| MEDLINE**| ID: mdl-30880478

##### RESUMO

BACKGROUND: The standard methods for measuring intracranial pressure (ICP) are invasive in nature. Non invasive methods such as ONSD may help circumvent these complications and may serve as a surrogate marker for increased ICP. The primary aim of this study was to assess the ONSD (optic nerve sheath diameter) changes using ultrasonography (USG) and computed tomography (CT) scan in hydrocephalus patients before and after the insertion of VP shunt. MATERIALS AND METHODS: A prospective observational study was conducted among 69 patients undergoing VP shunt surgery between the ages of 2 to 60 years. ONSD variation was measured by USG and CT scan both before and after the surgery. The difference in the pre-operative and post-operative ONSD measurement was analyzed using a paired t-test. Whereas, the measurements of ONSD were compared for agreement between two modalities (USG and CT) using Interclass correlation (ICC) and Bland Altman graph plot. RESULTS: Among 69 patients 38 were males, 31 were females and 12 were under the age of 10 years. In the adult group, average preoperative and postoperative ONSD measurement by USG was 5.80 ± 0.63 mm and 4.52 ± 0.72 (p < 0.001) and by CT was 5.77 ± 0.83 mm and 4.49 ± 0.76 mm (p < 0.001) respectively. Similarly, in the pediatric population, average preoperative and postoperative ONSD measurement by USG was found to be 4.76 ± 1.14 mm and 3.90 ± 1.08 mm and by CT was found to be 4.75+/-1.11 mm and 3.85 ± 1.09 mm respectively (p <0.001). CONCLUSION: In patients with hydrocephalus undergoing VP shunt surgery, we found a significant reduction in ONSD after the shunt insertion in both pediatric and adult population. We also found a good correlation between the USG and CT scan measurements of ONSD.

##### Assuntos

Hidrocefalia/cirurgia , Procedimentos Neurocirúrgicos/métodos , Nervo Óptico/diagnóstico por imagem , Derivação Ventriculoperitoneal , Adolescente , Adulto , Fatores Etários , Criança , Pré-Escolar , Feminino , Humanos , Pressão Intracraniana , Masculino , Pessoa de Meia-Idade , Período Pós-Operatório , Estudos Prospectivos , Tomografia Computadorizada por Raios X , Ultrassonografia , Adulto Jovem*J Phys Chem Lett ; 10(2): 144-149, 2019 Jan 17.*

**| MEDLINE**| ID: mdl-30569715

##### RESUMO

The photoelectron spectra of Sm2O- obtained over a range of photon energies exhibit anomalous changes in relative excited-state band intensities. Specifically, the excited-state transition intensities increase relative to the transition to the neutral ground state with decreasing photon energy, the opposite of what is expected from threshold effects. This phenomenon was previously observed in studies on several Sm-rich homo- and heterolanthanide oxides collected with two different harmonic outputs of a Nd:YAG (2.330 and 3.495 eV) [ J. Chem. Phys. 2017, 146, 194310]. We relate these anomalous intensities to populations of ground and excited anionic and neutrals states through the inspection of time-dependent perturbation theory within the adiabatic and sudden limits and for the first time show that transition intensities in photoelectron spectroscopy have a deep significance in gauging participation from excited states. We believe our results will have significance in the study of other electron-rich systems that have especially high density of accessible spin states.

*Environ Technol ; 40(6): 784-792, 2019 Feb.*

**| MEDLINE**| ID: mdl-29171794

##### RESUMO

In this study, potential microalgae species (Chlorella vulgaris, Scenedesmus dimorphus, Chlorococcum sp. and Chlamydomonas sp.) have been studied for nutrient removal from synthetic and industrial wastewater. Batch experiments were carried out to investigate the removal performance among four chosen species at different nitrogen and phosphorus concentrations. NH4-N and PO4-P were varied from 13.2 to 52.8 mg/L and 6.6 to 26.4 mg/L, respectively, by keeping N:P ratio as 2:1. In synthetic wastewater, maximum NH4-N and PO4-P removal efficiencies of 88.6% and 91.2% were obtained with C. vulgaris when compared to the other microalgae studied. Further studies were carried out using C. vulgaris in batch experiments to investigate the nutrient removal performance in secondary treated sewage, soak liquor and composite tannery effluent. Experimental results indicated that NH4-N, NO3-N, PO4-P and chemical oxygen demand (COD) removal efficiencies were found to be 68.6%, 74%, 71.5% and 90.2%, respectively, in secondary treated sewage. Maximum removal efficiencies of NH4-N, NO3-N, PO4-P and COD in composite tannery wastewater were found to be 55%, 85.6%, 60.5% and 43.4%, respectively. In soak liquor, maximum removal efficiencies of NH4-N, NO3-N, PO4-P and COD were found to 66.7%, 62.6%, 63.6% and 93.8%, respectively.

##### Assuntos

Chlorella vulgaris , Águas Residuárias , Nitrogênio , Nutrientes , Fósforo , Esgotos , Eliminação de Resíduos Líquidos*Diabet Med ; 36(9): 1118-1124, 2019 09.*

**| MEDLINE**| ID: mdl-30575096

##### RESUMO

AIM: To assess if latent autoimmune diabetes of adulthood (LADA) is associated with small fibre neuropathy. METHODS: Participants with LADA (n=31), Type 2 diabetes (n=31) and healthy control participants without diabetes (n=31) underwent a detailed assessment of neurologic deficits, quantitative sensory testing, electrophysiology, skin biopsy and corneal confocal microscopy. RESULTS: The groups were matched for age (healthy control without diabetes: 53.5±9.1 vs. Type 2 diabetes: 58.0±6.5 vs. LADA: 53.2±11.6 years), duration of diabetes (Type 2 diabetes: 10.0±8.3 vs. LADA: 11.0±9.1 years) and blood pressure. However, BMI (P=0.01) and triglycerides (P=0.0008) were lower and HbA1c (P=0.0005), total cholesterol (P=0.01) and HDL (P=0.002) were higher in participants with LADA compared with Type 2 diabetes. Peroneal motor nerve conduction velocity (P=0.04) and sural sensory nerve conduction velocity (P=0.008) were lower in participants with latent autoimmune diabetes in adults compared with Type 2 diabetes. Intra-epidermal nerve fibre density (P=0.008), corneal nerve fibre density (P=0.003) and corneal nerve branch density (P=0.006) were significantly lower in participants with LADA compared with Type 2 diabetes. There were no significant differences in the other neuropathy parameters. CONCLUSIONS: Despite comparable age and duration of diabetes, participants with LADA demonstrate more severe neuropathy and particularly small fibre neuropathy, compared with participants with Type 2 diabetes.

*J Chem Theory Comput ; 14(11): 5535-5552, 2018 Nov 13.*

**| MEDLINE**| ID: mdl-30335374

##### RESUMO

Weak interactions have a critical role in accurately portraying conformational change. However, the computational study of these often requires large basis electronic structure calculations that are generally cost-prohibitive within ab initio molecular dynamics. Here, we present a new approach to efficiently obtain AIMD trajectories in agreement with large, triple-Î¶, polarized valence basis functions, at much reduced computational cost. For example, it follows from our studies that AIMD trajectories can indeed be constructed in agreement with basis sets such as 6-311++G(2df,2pd) with computational effort commensurate with those from much smaller basis sets such as 6-31+G(d), for polypeptide systems with 100+ atoms. The method is based on molecular fragmentation and allows a range-specified repartitioning of intramolecular (and potentially intermolecular) interactions where noncovalent interactions are selectively assembled using a piece-wise reconstruction based on a set-theoretic inclusion-exclusion principle generalization of ONIOM. Through a simplex decomposition of molecular systems the approach efficiently provides the necessary many-body interactions to faithfully represent noncovalent interactions at the large basis limit. Conformational stabilization energies are provided at close to the complete-basis limit at much reduced cost, and similarly AIMD trajectories (both Born-Oppenheimer and Car-Parrinello-type) are obtained in agreement with very large basis set sizes, in an extremely efficient and accurate manner. The method is demonstrated through simulations on polypeptide fragments of a variety of sizes.

*Br J Anaesth ; 121(4): 978-979, 2018 Oct.*

**| MEDLINE**| ID: mdl-30236267

*J Chem Phys ; 149(5): 054305, 2018 Aug 07.*

**| MEDLINE**| ID: mdl-30089379

##### RESUMO

Lanthanide (Ln) oxide clusters have complex electronic structures arising from the partially occupied Ln 4f subshell. New anion photoelectron (PE) spectra of SmxCe3-xOy- (x = 0-3; y = 2-4) along with supporting results of density functional theory (DFT) calculations suggest interesting x and y-dependent Sm 4f subshell occupancy with implications for Sm-doped ionic conductivity of ceria, as well as the overall electronic structure of the heterometallic oxides. Specifically, the Sm centers in the heterometallic species have higher 4f subshell occupancy than the homonuclear Sm3Oy-/Sm3Oy clusters. The higher 4f subshell occupancy both weakens Sm-O bonds and destabilizes the 4f subshell relative to the predominantly O 2p bonding orbitals in the clusters. Parallels between the electronic structures of these small cluster systems with bulk oxides are explored. In addition, unusual changes in the excited state transition intensities, similar to those observed previously in the PE spectra of Sm2O- and Sm2O2- [J. O. Kafader et al., J. Chem. Phys. 146, 194310 (2017)], are also observed in the relative intensities of electronic transitions to excited neutral state bands in the PE spectra of SmxCe3-xOy- (x = 1-3; y = 2, 4). The new spectra suggest that the effect is enhanced with lower oxidation states and with an increasing number of Sm atoms, implying that the prevalence of electrons in the diffuse Sm 6s-based molecular orbitals and a more populated 4f subshell both contribute to this phenomenon. Finally, this work identifies challenges associated with affordable DFT calculations in treating the complex electronic structures exhibited by these systems, including the need for a more explicit treatment of strong coupling between the neutral and PE.

*J Skin Cancer ; 2018: 6061395, 2018.*

**| MEDLINE**| ID: mdl-29973992

##### RESUMO

Basosquamous carcinoma (BSC) is an uncommon skin malignancy with significant invasive and metastatic potential. There are currently no clear management guidelines. This study evaluates the management and outcomes of patients diagnosed with BSC over a 7-year period. We present an evidence-based unit protocol for the management of BSC. All patients treated for BSC between 2009 and 2015 were reviewed. Data collected included patient demographics, tumour-specific information, management strategy, presence of recurrence or metastasis, and details of follow-up. 74 patients were identified, making this one of the largest cohorts of BSC patients reported. Mean age at diagnosis was 75.4 years, with a male:female ratio of 1.6:1. The most common tumour site was the head and neck (n=43, 58.1%). All tumours were graded at pT1 (n=51) or pT2 (n=23). Inadequate excision occurred in 17 patients (23%). Mean excision margins were >4mm peripherally and deep. Inadequately excised BSCs were further treated with wide local excision (n=6) or radiotherapy (n=5), or both (n=1). There were no cases of local recurrence or metastatic disease. This study demonstrates a cohort of patients with BSCs that appear less aggressive than previously reported. Current management with surgical excision appears to produce adequate results. However, an evidence-based guideline is still lacking.

*J Chem Phys ; 149(3): 034502, 2018 Jul 21.*

**| MEDLINE**| ID: mdl-30037253

##### RESUMO

Thermodiffusion or the Ludwig-Soret effect is known as the cross effect between the temperature gradient and induced separation of mixture species in multicomponent mixtures. The performance of the boundary driven non-equilibrium molecular dynamics enhanced heat exchange (eHEX) algorithm was validated by evaluating the sign and magnitude of the thermodiffusion process in methane/n-butane/n-dodecane (nC1-nC4-nC12) ternary mixtures. The eHEX algorithm consists of an extended version of the HEX algorithm with an improved energy conservation property. In addition to this, the transferable potentials for phase equilibria-united atom augmented force field was employed in all molecular dynamics (MD) simulations to accurately represent molecular interactions in the fluid. Our newly employed MD algorithm was capable to appropriately reflect the thermophobicity concept and the coupled effect of relative density and mole fraction of the mixture species on the thermodiffusion process. The separation ratio of the ternary mixture for five different compositions (at 333.15 K and 35 MPa) showed good agreement with experimental data and better accuracy in predicting the sign change of the intermediate component (nC4) as its concentration in the mixture increases, when compared to other MD models.

*J Chem Theory Comput ; 14(6): 2852-2866, 2018 Jun 12.*

**| MEDLINE**| ID: mdl-29771516

##### RESUMO

We introduce a new coarse-graining technique for ab initio molecular dynamics that is based on the adaptive generation of connected geometric networks or graphs specific to a given molecular geometry. The coarse-grained nodes depict a local chemical environment and are networked to create edges, triangles, tetrahedrons, and higher order simplexes based on (a) a Delaunay triangulation procedure and (b) a method that is based on molecular, bonded and nonbonded, local interactions. The geometric subentities thus created, that is nodes, edges, triangles, and tetrahedrons, each represent an energetic measure for a specific portion of the molecular system, capturing a specific set of interactions. The energetic measure is constructed in a manner consistent with ONIOM and allows assembling an overall molecular energy that is purely based on the geometric network derived from the molecular conformation. We use this approach to obtain accurate MP2 energies for polypeptide chains containing up to 12 amino-acid monomers (123 atoms) and DFT energies up to 26 amino-acid monomers (263 atoms). The energetic measures are obtained at much reduced computational costs; the approach currently yields MP2 energies at DFT cost and DFT energies at PM6 cost. Thus, in essence the method performs an efficient "coarse-graining" of the molecular system to accurately reproduce the electronic structure properties. The method is comparable in principle to several fragmentation procedures recently introduced in the literature, including previous procedures introduced by two of the authors here, but critically differs by overcoming the computational bottleneck associated with adaptive fragment creation without spatial cutoffs. The method is used to derive a new, efficient, ab initio molecular dynamics formalism (both Born-Oppenheimer and Car-Parrinello-style extended Lagrangian schemes are presented) a critical hallmark of which is that, at each dynamics time-step, multiple electronic structure packages can be simultaneously invoked to assemble the energy and forces for the full system. Indeed, in this paper, as an illustration, we use both Psi4 and Gaussian09 simultaneously at every time-step to perform AIMD simulations and also the energetic benchmarks. The approach works in parallel (currently over 100 processors), and the computational implementation is object oriented in C++. MP2 and DFT based on-the-fly dynamics results are recovered to good accuracy from the coarse-grained AIMD methods introduced here at reduced costs as highlighted above.

##### Assuntos

Simulação de Dinâmica Molecular , Peptídeos/química , Ligações de Hidrogênio , Isomerismo , Peptídeos/metabolismo , Estrutura Secundária de Proteína , Termodinâmica*J Postgrad Med ; 64(1): 67-68, 2018.*

**| MEDLINE**| ID: mdl-29386419

*J Chem Theory Comput ; 14(1): 30-47, 2018 Jan 09.*

**| MEDLINE**| ID: mdl-29182347

##### RESUMO

We present two sampling measures to gauge critical regions of potential energy surfaces. These sampling measures employ (a) the instantaneous quantum wavepacket density, an approximation to the (b) potential surface, its (c) gradients, and (d) a Shannon information theory based expression that estimates the local entropy associated with the quantum wavepacket. These four criteria together enable a directed sampling of potential surfaces that appears to correctly describe the local oscillation frequencies, or the local Nyquist frequency, of a potential surface. The sampling functions are then utilized to derive a tessellation scheme that discretizes the multidimensional space to enable efficient sampling of potential surfaces. The sampled potential surface is then combined with four different interpolation procedures, namely, (a) local Hermite curve interpolation, (b) low-pass filtered Lagrange interpolation, (c) the monomial symmetrization approximation (MSA) developed by Bowman and co-workers, and (d) a modified Shepard algorithm. The sampling procedure and the fitting schemes are used to compute (a) potential surfaces in highly anharmonic hydrogen-bonded systems and (b) study hydrogen-transfer reactions in biogenic volatile organic compounds (isoprene) where the transferring hydrogen atom is found to demonstrate critical quantum nuclear effects. In the case of isoprene, the algorithm discussed here is used to derive multidimensional potential surfaces along a hydrogen-transfer reaction path to gauge the effect of quantum-nuclear degrees of freedom on the hydrogen-transfer process. Based on the decreased computational effort, facilitated by the optimal sampling of the potential surfaces through the use of sampling functions discussed here, and the accuracy of the associated potential surfaces, we believe the method will find great utility in the study of quantum nuclear dynamics problems, of which application to hydrogen-transfer reactions and hydrogen-bonded systems is demonstrated here.

*IEEE/ACM Trans Comput Biol Bioinform ; 15(2): 411-421, 2018.*

**| MEDLINE**| ID: mdl-26955051

##### RESUMO

Phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of species and genes and other dependent entities. Reconciliation is typically performed in a maximum parsimony framework and the number of optimal reconciliations can grow exponentially with the size of the trees, making it difficult to understand the solution space. This paper demonstrates how a small number of reconciliations can be found that collectively contain the most highly supported events in the solution space. While we show that the formal problem is NP-complete, we give a approximation algorithm, experimental results that indicate its effectiveness, and the new DTL-RnB software tool that uses our algorithms to summarize the space of optimal reconciliations (www.cs.hmc.edu/dtlrnb).

##### Assuntos

Algoritmos , Biologia Computacional/métodos , Modelos Genéticos , Filogenia , Software*Environ Technol ; 39(19): 2434-2446, 2018 Oct.*

**| MEDLINE**| ID: mdl-28707563

##### RESUMO

The removal of phenol sulfonic acid-syntan (PSAS) in terms of chemical oxygen demand (COD) was studied at different pH, ozone and initial PSAS concentrations and the optimum condition was found to be pH 7, ozone concentration of 5.2 × 10-3â mmol/L and initial PSAS concentration of 500â mg/L. The increase in BOD5/COD ratio confirmed the bio-treatability of ozonated PSAS effluent. The excitation-emission matrix intensity and Fourier transmission infra-red spectroscopy confirmed the generation of intermediate by-product during degradation of PSAS. The ozonation of PSAS was found to obey fast regime pseudo-first-order reaction with a rate constant of 3.7 × 10-9â mol-1â s-1. The mean oxidation state of carbon value between +2 and +3 confirmed that the ozonation of PSAS resulted in partial mineralization.