Evaluation of machine-learning methods for ligand-based virtual screening

Machine-learning methods can be used for virtual screening by analysing the structural characteristics of molecules of known (in)activity, and we here discuss the use of kernel discrimination and naive Bayesian classifier (NBC) methods for this purpose. We report a kernel method that allows the processing of molecules represented by binary, integer and real-valued descriptors, and show that it is little different in screening performance from a previously described kernel that had been developed specifically for the analysis of binary fingerprint representations of molecular structure. We then evaluate the performance of an NBC when the training-set contains only a very few active molecules. In such cases, a simpler approach based on group fusion would appear to provide superior screening performance, especially when structurally heterogeneous datasets are to be processed

Reproducibility and validity of the food frequency questionnaire for estimating habitual dietary intake in children and adolescents

<p>Abstract</p> <p>Background</p> <p>A previous study reported the development a 75-item food frequency questionnaire for Japanese children (CFFQ). The first aim was to examine the reproducibility and validity of the CFFQ in order to assess dietary intake among two groups; 3-11 year old children (YC group) and 12-16 year old children (AD group). The second aim was to use the CFFQ and the FFQ for adults (AFFQ), and to determine which was better suited for assessing the intake of children in each group.</p> <p>Methods</p> <p>A total of the 103 children participated in this study. The interval between the first CFFQ and AFFQ and the second CFFQ and AFFQ was one month. Four weighted dietary records (WDRs) were conducted once a week. Pearson's correlation coefficients between the first and second FFQs were calculated to test the reproducibility of each FFQ. Pearson's correlation coefficients between WDRs and the second FFQ were calculated for the unadjusted value and sex-, age-, and energy-adjusted values to determine the validity of each FFQ.</p> <p>Results</p> <p>The final number of subjects participating in the analysis was 89. The median correlation coefficients between the first and second CFFQs and AFFQs were 0.76 and 0.73, respectively. There was some over/underestimation of nutrients in the CFFQ of the YC group and in the AFFQ of the AD group. The medians of the sex-, age-, and energy-adjusted correlation coefficients were not different between the YC and AD groups for each FFQ. The correlation coefficient in sex-, age-, and energy-adjusted value revealed that the largest number of subject with high (0.50 or more) value was obtained by the CFFQ in the YC group.</p> <p>Conclusions</p> <p>This study indicated that the CFFQ might be a useful tool for assessing habitual dietary intake of children in the YC group. Although the CFFQ agreed moderately with habitual intake, it was found to underestimate intake in theAD group. However, for the AFFQ, the ability to rank habitual intake was low. Therefore, it is necessary to develop a new FFQ or modify an existing FFQ to accurately assess the habitual diet of children in the AD group.</p

Paired and clustered quantum Hall states

We briefly summarize properties of quantum Hall states with a pairing or clustering property. Their study employs a fundamental connection with parafermionic Conformal Field Theories. We report on closed form expressions for the many-body wave functions and on multiplicities of the fundamental quasi-hole excitations.Comment: 13 pages, Contribution to the proceedings of the NATO Advanced Research Workshop "Statistical Field Theories" Como (Italy), June 18-23 200

Tracing Sagittarius Structure with SDSS and SEGUE Imaging and Spectroscopy

We show that the Sagittarius dwarf tidal stream can be traced with very red K/M-giant stars selected from SDSS photometry. A subset of these stars are spectroscopically confirmed with SEGUE and SDSS spectra, and the distance scale of 2MASS and SDSS M giants is calibrated to the RR Lyrae distance scale. The absolute g band magnitude of the K/M-giant stars at the tip of the giant branch is M_g=-1.0. The line-of-sight velocities of the M giant and BHB stars that are spatially coincident with the Sgr dwarf tidal stream are consistent with those of previous authors, reinforcing the need for new models that can explain all of the Sgr tidal debris stream observations. We estimate stellar densities along the tidal tails that can be used to help constrain future models. The K/M-giant, BHB, and F-turnoff stars in the lower surface brightness tidal stream that is adjacent to the main leading Sgr dwarf tidal tail have velocities and metallicities that are similar to those of the stars in the leading tidal tail. The ratio of K/M giants to BHBs and BHBs to F-turnoff stars are also similar for both branches of the leading tidal tail. We show that there is an additional low-metallicity tidal stream near the Sgr trailing tidal tail.Comment: 19 figures, accepted for publication in ApJ, references update

Diet, body size and menarche in a multiethnic cohort

A multiethnic cohort of 1378 Southern California school girls aged 8–13 years was followed for 4 years to evaluate factors predicting age at menarche, a risk factor for breast cancer. Height and weight were measured and dietary intake was assessed using a semi-quantitative food frequency questionnaire. Of 939 girls providing data on menarcheal status, 767 were premenarcheal at the start of the study; 679 girls provided acceptable dietary data and were included in the analyses. Cox proportional hazards models were used to assess the relationship between diet, body size, ethnicity and age at menarche. Hispanic, Asian/Pacific Island and African-American girls were more likely to experience early menarche than non-Hispanic white girls. Tall (> 148.6 cm) versus short (< 135.9 cm) girls experienced earlier menarche (relative hazard (RH) = 2.9, 95% confidence interval (CI) 2.1–4.1) as did those with high Quetelet's index (QI, kg m−2) (> 20.7) versus low QI (< 16.1) (RH = 2.2, 95% CI 1.7–2.9). Of all the dietary variables analysed, only energy intake was related to age at menarche. High versus low energy intake (> 12013 kJ vs < 7004 kJ) was associated with a delay in menarche (RH = 0.7, 95% CI 0.5–0.9); this finding was limited to a subset of heavy Hispanic girls who appeared to underreport their dietary intake. © 1999 Cancer Research Campaig

2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope

<p>Abstract</p> <p>Background</p> <p>Quantitative structure-activity relationships (QSAR) analysis of peptides is helpful for designing various types of drugs such as kinase inhibitor or antigen. Capturing various properties of peptides is essential for analyzing two-dimensional QSAR. A descriptor of peptides is an important element for capturing properties. The atom pair holographic (APH) code is designed for the description of peptides and it represents peptides as the combination of thirty-six types of key atoms and their intermediate binding between two key atoms.</p> <p>Results</p> <p>The substructure pair descriptor (SPAD) represents peptides as the combination of forty-nine types of key substructures and the sequence of amino acid residues between two substructures. The size of the key substructures is larger and the length of the sequence is longer than traditional descriptors. Similarity searches on C5a inhibitor data set and kinase inhibitor data set showed that order of inhibitors become three times higher by representing peptides with SPAD, respectively. Comparing scope of each descriptor shows that SPAD captures different properties from APH.</p> <p>Conclusion</p> <p>QSAR/QSPR for peptides is helpful for designing various types of drugs such as kinase inhibitor and antigen. SPAD is a novel and powerful descriptor for various types of peptides. Accuracy of QSAR/QSPR becomes higher by describing peptides with SPAD.</p

Magnesium intake and colorectal cancer risk in the Netherlands Cohort Study

Energy-adjusted magnesium intake was nonsignificantly inversely related to risk of colorectal cancer (n=2328) in the Netherlands Cohort Study on Diet and Cancer that started in 1986 (n=58 279 men and 62 573 women). Statistically significant inverse trends in risk were observed in overweight subjects for colon and proximal colon cancer across increasing quintiles of magnesium uptake (P-trend, 0.05 and 0.02, respectively). Although an overall protective effect was not afforded, our results suggest an effect of magnesium in overweight subjects, possibly through decreasing insulin resistance

Towards identification of a non-abelian state: observation of a quarter of electron charge at ν=5/2\nu=5/2 quantum Hall state

The fractional quantum Hall effect, where plateaus in the Hall resistance at values of coexist with zeros in the longitudinal resistance, results from electron correlations in two dimensions under a strong magnetic field. Current flows along the edges carried by charged excitations (quasi particles) whose charge is a fraction of the electron charge. While earlier research concentrated on odd denominator fractional values of $\nu$, the observation of the even denominator $\nu=5/2$ state sparked a vast interest. This state is conjectured to be characterized by quasiparticles of charge e/4, whose statistics is non-abelian. In other words, interchanging of two quasi particles may modify the state of the system to an orthogonal one, and does not just add a phase as in for fermions or bosons. As such, these quasiparticles may be useful for the construction of a topological quantum computer. Here we report data of shot noise generated by partitioning edge currents in the $\nu=5/2$ state, consistent with the charge of the quasiparticle being e/4, and inconsistent with other potentially possible values, such as e/2 and e. While not proving the non-abelian nature of the $\nu=5/2$ state, this observation is the first step toward a full understanding of these new fractional charges

Health, ageing and private health insurance: baseline results from the 45 and Up Study cohort

Correction to Banks E, Jorm L, Lujic S, Rogers K. Health, ageing and private health insurance: baseline results from the 45 and Up Study cohort. ANZ Health Policy 2009; 6: 16