Sample selection models for count data in R

We provide a detailed hands-on tutorial for the R package SemiParSampleSel (version 1.5). The package implements selection models for count responses fitted by penalized maximum likelihood estimation. The approach can deal with non-random sample selection, flexible covariate effects, heterogeneous selection mechanisms and varying distributional parameters. We provide an overview of the theoretical background and then demonstrate how SemiParSampleSel can be used to fit interpretable models of different complexity. We use data from the German Socio-Economic Panel survey (SOEP v28, 2012. doi: 10.5684/soep.v28) throughout the tutorial

A Beta-binominal Regression Model to Predict Doppler Score on Ultrasound Examination in Patients With Inflammatory Hand Joint Pain

BACKGROUND: US assessment of small joints is essential for the diagnosis of polyarticular inflammatory arthritis and guidance of the therapeutic decisions in patients with established RA. The access to US varies among hospitals and rheumatology services. Even if a considerable proportion of patients with hand joint pain or established RA might have subclinical inflammation, it is not cost-effective to screen them all. The aim of our study was to build a statistical model to assess the influence of several outcome measures (such as number of tender joints (TJC) and swollen joints (SJC) out of 28, global visual analogue scale (GVAS), CRP, ESR, presence of RF and anti-CCP antibodies, disease duration and medication) on the presence of a power Doppler signal at the US examination of hand joints. METHODS: We proposed a regression model to assess the contribution of every outcome measure to the risk of having active joint inflammation as well as predict the power Doppler signal. We excluded patients with a power Doppler signal present in more than 10/22 joints to ensure homogeneity in the data. We conducted a real-life study including 276 patients referred for the suspicion of active joint inflammation (new referrals for the suspicion of inflammatory arthritis, RA patients and patients with other inflammatory rheumatic conditions). We assessed 22 hand joints in every patient, irrespective of their hand symptoms, using the OMERACT scoring system for power Doppler signal. All patients had clinical assessments and laboratory tests within 2 weeks from the US scan. The proposed regression model was based on a beta-binomial distribution (1, disease present; 0, disease absent) for the power Doppler score variable and a mix of main interaction effects for the outcome measures stated above. Negative interaction effects showed that the respective outcome was associated with a lower number of joints with power Doppler signal. RESULTS:Table 1 summarizes the marginal effects of different variables on the number of joints with Doppler signal at the US examination in newly referred patients for the suspicion of inflammatory arthritis or previous diagnosis of RA, and patients with other inflammatory conditions

Feasibility of identifying families for genetic studies of birth defects using the National Health Interview Survey

BACKGROUND: The purpose of this study was to determine whether the National Health Interview Survey is a useful source to identify informative families for genetic studies of birth defects. METHODS: The 1994/1995 National Health Interview Survey (NHIS) was used to identify households where individuals with two or more birth defects reside. Four groups of households were identified: 1) single non-familial (one individual with one birth defect); 2) single familial (more than one individual with one birth defect); 3) multiple non-familial (one individual with more than one birth defect), and 4) multiple familial (more than one individual with more than one birth defect). The March 2000 U.S. Census on households was used to estimate the total number of households in which there are individuals with birth defects. RESULTS: Of a total of 28,094 households and surveyed about birth defects and impairments, 1,083 single non-familial, 55 multiple non-familial, 54 single familial, and 8 multiple familial households were identified. Based on the 2000 U.S. census, it is estimated that there are 4,472,385 households where at least one person has one birth defect in the United States and in 234,846 of them there are at least two affected individuals. Western states had the highest prevalence rates. CONCLUSIONS: Population-based methods, such as the NHIS, are modestly useful to identify the number and the regions where candidate families for genetic studies of birth defects reside. Clinic based studies and birth defects surveillance systems that collect family history offer better probability of ascertainment

Evaluating Impact of Risk Associated Outcomes on Ultrasound Doppler Score of Patients with Inflammatory Hand Joint Pain Using a Beta-Binomial Model

Abstract SAT0603 published in the Annals of the Rheumatic Diseases, vol 74 (S2), page 880, June 2015

Search for genetic factors predisposing to atherogenic dyslipidemia

BACKGROUND: Atherogenic dyslipidemia (AD) is a common feature in persons with premature coronary heart disease. While several linkage studies have been carried out to dissect the genetic etiology of lipid levels, few have investigated the AD lipid triad comprising elevated serum triglyceride, small low density lipoprotein (LDL) particles, and reduced high density lipoprotein (HDL) cholesterol levels. Here we report the results of a whole-genome screen for AD using the Framingham Heart Study population. RESULTS: Our analyses provide some evidence for linkage to AD on chromosomes 1q31, 3q29, 10q26, 14p12, 14q13, 16q24, 18p11, and 19q13. CONCLUSION: AD susceptibility is modulated by multiple genes in different chromosomes. Our study confirms results from other populations and suggests new areas of potential importance

Genome-wide screen for heavy alcohol consumption

BACKGROUND: To find specific genes predisposing to heavy alcohol consumption (self-reported consumption of 24 grams or more of alcohol per day among men and 12 grams or more among women), we studied 330 families collected by the Framingham Heart Study made available to participants in the Genetic Analysis Workshop 13 (GAW13). RESULTS: Parametric and nonparametric methods of linkage analysis were used. No significant evidence of linkage was found; however, weak signals were identified in several chromosomal regions, including 1p22, 4q12, 4q25, and 11q24, which are in the vicinity of those reported in other similar studies. CONCLUSION: Our study did not reveal significant evidence of linkage to heavy alcohol use; however, we found weak confirmation of studies carried out in other populations

A highly stable atomic vector magnetometer based on free spin precession

We present a magnetometer based on optically pumped Cs atoms that measures the magnitude and direction of a 1 $\mu$T magnetic field. Multiple circularly polarized laser beams were used to probe the free spin precession of the Cs atoms. The design was optimized for long-time stability and achieves a scalar resolution better than 300 fT for integration times ranging from 80 ms to 1000 s. The best scalar resolution of less than 80 fT was reached with integration times of 1.6 to 6 s. We were able to measure the magnetic field direction with a resolution better than 10 $\mu$rad for integration times from 10 s up to 2000 s

Constraining interactions mediated by axion-like particles with ultracold neutrons

We report a new limit on a possible short range spin-dependent interaction from the precise measurement of the ratio of Larmor precession frequencies of stored ultracold neutrons and $^{199}$Hg atoms confined in the same volume. The measurement was performed in a $\sim$1$\mu$ T vertical magnetic holding field with the apparatus searching for a permanent electric dipole moment of the neutron at the Paul Scherrer Institute. A possible coupling between freely precessing polarized neutron spins and unpolarized nucleons of the wall material can be investigated by searching for a tiny change of the precession frequencies of neutron and mercury spins. Such a frequency change can be interpreted as a consequence of a short range spin-dependent interaction that could possibly be mediated by axions or axion-like particles. The interaction strength is proportional to the CP violating product of scalar and pseudoscalar coupling constants $g_Sg_P$. Our result confirms limits from complementary experiments with spin-polarized nuclei in a model-independent way. Limits from other neutron experiments are improved by up to two orders of magnitude in the interaction range of $10^{-6}<\lambda<10^{-4}$ m

Interaction between GRIP and Liprin-α/SYD2 Is Required for AMPA Receptor Targeting

Interaction with the multi-PDZ protein GRIP is required for the synaptic targeting of AMPA receptors, but the underlying mechanism is unknown. We show that GRIP binds to the liprin-α/SYD2 family of proteins that interact with LAR receptor protein tyrosine phosphatases (LAR-RPTPs) and that are implicated in presynaptic development. In neurons, liprin-α and LAR-RPTP are enriched at synapses and coimmunoprecipitate with GRIP and AMPA receptors. Dominant-negative constructs that interfere with the GRIP-liprin interaction disrupt the surface expression and dendritic clustering of AMPA receptors in cultured neurons. Thus, by mediating the targeting of liprin/GRIP-associated proteins, liprin-α is important for postsynaptic as well as presynaptic maturation

Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase

The prokaryotic DNA(cytosine-5)methyltransferase M.SssI shares the specificity of eukaryotic DNA methyltransferases (CG) and is an important model and experimental tool in the study of eukaryotic DNA methylation. Previously, M.SssI was shown to be able to catalyze deamination of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing from the reaction. To test whether this side-activity of the enzyme can be used to distinguish between unmethylated and C5-methylated cytosines in CG dinucleotides, we re-investigated, using a sensitive genetic reversion assay, the cytosine deaminase activity of M.SssI. Confirming previous results we showed that M.SssI can deaminate cytosine to uracil in a slow reaction in the absence of SAM and that the rate of this reaction can be increased by the SAM analogue 5’-amino-5’-deoxyadenosine. We could not detect M.SssI-catalyzed deamination of C5-methylcytosine (m5C). We found conditions where the rate of M.SssI mediated C-to-U deamination was at least 100-fold higher than the rate of m5C-to-T conversion. Although this difference in reactivities suggests that the enzyme could be used to identify C5-methylated cytosines in the epigenetically important CG dinucleotides, the rate of M.SssI mediated cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction. Amino acid replacements in the presumed SAM binding pocket of M.SssI (F17S and G19D) resulted in greatly reduced methyltransferase activity. The G19D variant showed cytosine deaminase activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase activity was also detectable in an E. coli ung+ host proficient in uracil excision repair