Two-dimensional matrix algorithm using detrended fluctuation analysis to distinguish Burkitt and diffuse large B-cell lymphoma

Copyright © 2012 Rong-Guan Yeh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.A detrended fluctuation analysis (DFA) method is applied to image analysis. The 2-dimensional (2D) DFA algorithms is proposed for recharacterizing images of lymph sections. Due to Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), there is a significant different 5-year survival rates after multiagent chemotherapy. Therefore, distinguishing the difference between BL and DLBCL is very important. In this study, eighteen BL images were classified as group A, which have one to five cytogenetic changes. Ten BL images were classified as group B, which have more than five cytogenetic changes. Both groups A and B BLs are aggressive lymphomas, which grow very fast and require more intensive chemotherapy. Finally, ten DLBCL images were classified as group C. The short-term correlation exponent α1 values of DFA of groups A, B, and C were 0.370 ± 0.033, 0.382 ± 0.022, and 0.435 ± 0.053, respectively. It was found that α1 value of BL image was significantly lower (P < 0.05) than DLBCL. However, there is no difference between the groups A and B BLs. Hence, it can be concluded that α1 value based on DFA statistics concept can clearly distinguish BL and DLBCL image.National Science Council (NSC) of Taiwan the Center for Dynamical Biomarkers and Translational Medicine, National Central University, Taiwan (also sponsored by National Science Council)

Effects of Helix Dipole Membrane Field Potential Interactions on Hydrophobic Energies of Transmembrane Proteins

The race to uncover new biological drug targets has led to an emerging field of research on the thermodynamic properties that stabilize transmembrane proteins as well as the role of these stabilizing factors in shaping the evolutionary landscape of drug target populations. When proteins are inserted into the plasma membrane, they fold into three- dimensional secondary protein structures called alpha helices. The electrical interactions within the alpha helix causes the protein to form a macrodipole. As a result of this phenomenon, the energetic stabilities of TM proteins may either be disrupted or enhanced due to the interactions between the surrounding membrane potential and the charged dipole termini of the folded helix. Currently, the relative contributions of compensatory factors to TM protein stability and their population distributions are poorly understood. In this study, two categories of bitopic proteins and the hydrophobic energies of their TM domains were investigated. We hypothesized that Type I TM proteins exhibit lower hydrophobic free energies as a compensatory response to the decreased electrical stabilities of Type I proteins that have incurred an energetic penalty due to the spatial orientations. A Z test showed that Type I proteins exhibit significantly lower hydrophobic free energies than Type II proteins (p = 0.0003, α = 0.05). A Z test of Shannon entropies of both protein types revealed that Type 1 proteins exhibit significantly lower Shannon entropies than those of Type 2 (p = 0.000, α = 0.05). Linear regression analysis showed a weak correlation between Type I Shannon entropies and Type I hydrophobic energies (R2 = 0.221) and Type II Shannon entropies and Type II hydrophobic energies (R2 = 0.232), suggesting that Shannon entropies are not a direct function of hydrophobic free energies and may arise from synergistic interactions among various energetic contributors.I. INTRODUCTION.1 | II. REVIEW OF LITERATURE 6 | Type I and Type II Proteins 6 | The Alpha Helix Dipole .7 | Electrical Properties of Cellular Membranes .11 | Determinants of Protein Stability 13 | Hydrophobicity Scales 15 | Functional Significance of Transmembrane Domains .16 | III. MATERIALS AND METHODS .18 | Data Collection. 18 | Retrieval of Type I and Type II Protein Accession Numbers 18 | Retrieval of Transmembrane Domain Residue Sequences .18 | Retrieval of Grand Average of Hydropathicity Values .19 | Retrieval of Kyte and Doolittle Hydropathy Indices 19 | Retrieval and Determination of Protein Functional Class 20 | Mathematical Computation .20 | Computation of Gibb’s Free Energy .20 | Computation of Hydrophobic Energies 20 | Computation of Shannon Entropies 21 | Statistical Analysis 22 | Monte Carlo Simulation of Normal Distribution of Hydrophobic Energies 22 | Shapiro Wilk Test of Gaussian Normality of Hydrophobic Energies .22 | Levene’s Test of Equality of Variances of Hydrophobic Energies .23 | Mann-Whitney U Test of Hydrophobic Energies .23 | Z Test of Hydrophobic Energies .24 | Monte Carlo Simulation of Normal Distribution of Shannon Entropies 24 | Shapiro Wilk Test of Gaussian Normality of Shannon Entropies .25 | Levene’s Test of Equality of Variances of Shannon Entropies .25 | Mann-Whitney U Test of Shannon Entropies 25 | Z Test of Shannon Entropies .26 | Linear Regression of Hydrophobic Energies and Shannon Entropies 27 | IV. RESULTS28 | Gibb’s Free Energy Difference 28 | Frequency Distributions of Hydrophobic Energies .28 | Mann-Whitney U Test of Hydrophobic Energies 30 | Z Test of Hydrophobic Energies 32 | Frequency Distributions of Shannon Entropies .32 | Mann-Whitney U Test of Shannon Entropies 34 | Z Test of Shannon Entropies 36 | Shannon Entropy as a Function of Hydrophobic Energy 36 | Functional Classification .39 | V. DISCUSSION. 40 | Hydrophobic Energy Compensation 40 | Z Test of Transmembrane Domain Hydrophobic Energies .40 | Z Test of Transmembrane Domain Shannon Entropies .41 | Linear Regression Analysis of Shannon Entropy as a Function of Hydrophobic | Energy 42 | Functional Classification .43 | Summary. 43 | REFERENCES.45 | APPENDIX A: Kyte and Doolittle Amino Acid Hydrophobicity Indices 49 | APPENDIX B: Type I Hydrophobic Energies and Shannon Entropies 51|Kang, JonghoonGrove, Theresa J.Gosnell, DonnaLaPlant, James T.M.S.Biolog

Little String Theory from Double-Scaling Limits of Field Theories

We show that little string theory on S^5 can be obtained as double-scaling limits of the maximally supersymmetric Yang-Mills theories on RxS^2 and RxS^3/Z_k. By matching the gauge theory parameters with those in the gravity duals found by Lin and Maldacena, we determine the limits in the gauge theories that correspond to decoupling of NS5-brane degrees of freedom. We find that for the theory on RxS^2, the 't Hooft coupling must be scaled like ln^3(N), and on RxS^3/Z_k, like ln^2(N). Accordingly, taking these limits in these field theories gives Lagrangian definitions of little string theory on S^5.Comment: 16 pages, 5 figures. Minor change

Biocatalytic preparation and absolute configuration of enantiomerically pure fungistatic anti-2-benzylindane derivatives. Study of the detoxification mechanism by Botrytis cinerea

Enantiomerically pure 2-benzylindane derivatives were prepared using biocatalytic methods and their absolute configuration determined. (1R,2S)-2-Benzylindan-1-ol ((1R,2S)-2) and (S)-2-benzylindan-1-one ((S)-3) were produced by fermenting baker’s yeast. Lipase-mediated esterifications and hydrolysis of the corresponding racemic substrates gave rise to the enantiopure compounds (1S,2R)-2-benzylindan-1-ol ((1S,2R)-2) and (1R,2S)-2-benzylindan-1-ol ((1R,2S)-2), respectively. The antifungal activity of these products against two strains of the plant pathogen Botrytis cinerea was tested. The metabolism of anti-(±)-2-benzylindan-1-ol (anti-(±)-2) by B. cinerea as part of the fungal detoxification mechanism is also described and revealed interesting differences in the genome of both strains

Coarse-Graining the Lin-Maldacena Geometries

The Lin-Maldacena geometries are nonsingular gravity duals to degenerate vacuum states of a family of field theories with SU(2|4) supersymmetry. In this note, we show that at large N, where the number of vacuum states is large, there is a natural `macroscopic' description of typical states, giving rise to a set of coarse-grained geometries. For a given coarse-grained state, we can associate an entropy related to the number of underlying microstates. We find a simple formula for this entropy in terms of the data that specify the geometry. We see that this entropy function is zero for the original microstate geometries and maximized for a certain ``typical state'' geometry, which we argue is the gravity dual to the zero-temperature limit of the thermal state of the corresponding field theory. Finally, we note that the coarse-grained geometries are singular if and only if the entropy function is non-zero.Comment: 29 pages, LaTeX, 3 figures; v2 references adde

Availability of pediatric and neonatal intensive care units in the city of São Paulo

OBJECTIVE: To describe the health care service provided in pediatric intensive care units in the city of São Paulo, by identifying and describing the units and analyzing their geographic distribution. METHODS: A descriptive cross-sectional study was carried out during a two-year period (August 2000 to July 2002). Data were collected through questionnaires answered by medical directors of each pediatric and neonatal intensive care unit. RESULTS: São Paulo is served by 107 pediatric and neonatal intensive care units, of which 85 (79.4%) completed and returned the questionnaire. We found a very unequal distribution of units as there were more units in places with the least pediatric population. Regarding to pediatric intensive care units specialization, 7% were pediatric, 41.2% were neonatal and 51.7% were mixed (pediatric and neonatal). Regarding hospital funds, 15.3% were associated with philanthropic institutions, 37.6% were private and 47% were public. A total of 1,067 beds were identified, of which 969 were active. The ratio bed/patient aged 0-14 was 1/2,728, varying from 1/604 at health districts - I to 1/6,812 at health districts - III. The units reported an average of 11.7 beds (2 to 60). The neonatal intensive care unit had a median of 16.9 beds per unit and pediatric intensive care units a median of 8.5 beds/unit. CONCLUSION: In São Paulo, we found an uneven distribution of pediatric and neonatal intensive care units among the health districts. There was also an uneven distribution between public and private units, and neonatal and pediatric ones. The current report is the first step in the effort to improve the quality of medical assistance in pediatric and neonatal intensive care units in São Paulo.OBJETIVO: Caracterizar a assistência de saúde prestada em tratamento intensivo pediátrico e neonatal no município de São Paulo através da identificação, descrição e distribuição geográfica das unidades. MÉTODOS: Estudo descritivo, tipo transversal, onde foram estudadas as unidades de terapia intensiva pediátrica e neonatal do município de São Paulo, no período de agosto de 2000 a julho de 2002. A coleta dos dados foi realizada por meio de questionário preenchido pelo coordenador médico de cada unidade. RESULTADOS: Foram listadas 107 unidades de terapia intensiva pediátricas e neonatais no município de São Paulo. Oitenta e cinco (79,4%) unidades forneceram os dados, constituindo a população de estudo. Observou-se maior número de unidades de terapia intensiva em Núcleos Regionais de Saúde com menor população pediátrica. Quanto à faixa etária, 7% eram exclusivamente pediátricas, 41,2% neonatais, e 51,7% mistas. Em relação ao mantenedor: 47% eram públicas, 37,6% privadas, e 15,3% filantrópicas. Identificamos 1.067 leitos, estando 969 em atividade. A razão leito/paciente de 0 a 14 anos foi de 1:2.728, variando de 1:604 (Núcleo Regional de Saúde - I) a 1:6.812 (Núcleo Regional de Saúde - III). O número de leitos por unidade variou de 2 a 60, com média de 11,7 (unidades de terapia intensiva neonatais: 16,9; mistas: 8,5). CONCLUSÃO: No município de São Paulo, observou-se uma distribuição desproporcional das unidades de terapia intensiva pediátrica e neonatal entre os cinco Núcleos Regionais de Saúde. Houve também uma distribuição desproporcional entre unidades de terapia intensiva públicas e privadas e entre neonatais e pediátricas. Esse estudo foi o primeiro esforço na busca por melhor qualidade na assistência intensiva pediátrica e neonatal no município de São Paulo.Universidade de São Paulo Faculdade de MedicinaUniversidade Federal de São Paulo (UNIFESP) Departamento de PediatriaUniversidade de São Paulo Hospital Universitário Unidade de Terapia Intensiva PediátricaUNIFESP, Depto. de PediatriaSciEL

On the existence of supergravity duals to D1--D5 CFT states

We define a metric operator in the 1/2-BPS sector of the D1-D5 CFT, the eigenstates of which have a good semi-classical supergravity dual; the non-eigenstates cannot be mapped to semi-classical gravity duals. We also analyse how the data defining a CFT state manifests itself in the gravity side, and show that it is arranged into a set of multipoles. Interestingly, we find that quantum mechanical interference in the CFT can have observable manifestations in the semi-classical gravity dual. We also point out that the multipoles associated to the normal statistical ensemble fluctuate wildly, indicating that the mixed thermal state should not be associated to a semi-classical geometry.Comment: 22 pages, 2 figures. v2 : references added, typos correcte