Methodological Considerations for Comparison of Cross-species Use of Tactile Contact

Cross-species comparisons are benefited by compatible datasets; conclusions related to phylogenetic comparisons, questions on convergent and divergent evolution, or homologs versus analogs can only be made when the behaviors being measured are comparable. A direct comparison of the social function of physical contact across two disparate taxa is possible only if data collection and analyses methodologies are analogous. We identify and discuss the parameters, assumptions and measurement schemes applicable to multiple taxa and species that facilitate cross-species comparisons. To illustrate our proposed guidelines for evaluating the role played by tactile contact in social behavior across disparate taxa, this paper presents data on mother-offspring relationships in the two species studied by the authors: chimpanzees (Pan troglodytes schweinfurthii) and dolphins (bottlenose and spotted, Tursiops truncatus and Stenella frontalis, respectively). Cross-species comparative studies allow for a more comprehensive assessment of the similarities and differences with respect to how animals traverse the relationships that form their social groups and societies

Competition for finite resources

The resources in a cell are finite, which implies that the various components of the cell must compete for resources. One such resource is the ribosomes used during translation to create proteins. Motivated by this example, we explore this competition by connecting two totally asymmetric simple exclusion processes (TASEPs) to a finite pool of particles. Expanding on our previous work, we focus on the effects on the density and current of having different entry and exit rates.Comment: 15 pages, 9 figures, v2: minor revisions, v3: additional reference & minor correction

A beamforming video recorder for integrated observations of dolphin behavior and vocalizations

Author Posting. © Acoustical Society of America, 2005. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 117 (2005): 1005-1008, doi:10.1121/1.1831284.In this Letter we describe a beamforming video recorder consisting of a video camera at the center of a 16 hydrophone array. A broadband frequency-domain beamforming algorithm is used to estimate the azimuth and elevation of each detected sound. These estimates are used to generate a visual cue indicating the location of the sound source within the video recording, which is synchronized to the acoustic data. The system provided accurate results in both lab calibrations and a field test. The system allows researchers to correlate the acoustic and physical behaviors of marine mammals during studies of social interactions.This research was funded by NSF Ocean Sciences CAREER award 9733391

Dynamical Transition in the Open-boundary Totally Asymmetric Exclusion Process

We revisit the totally asymmetric simple exclusion process with open boundaries (TASEP), focussing on the recent discovery by de Gier and Essler that the model has a dynamical transition along a nontrivial line in the phase diagram. This line coincides neither with any change in the steady-state properties of the TASEP, nor the corresponding line predicted by domain wall theory. We provide numerical evidence that the TASEP indeed has a dynamical transition along the de Gier-Essler line, finding that the most convincing evidence was obtained from Density Matrix Renormalisation Group (DMRG) calculations. By contrast, we find that the dynamical transition is rather hard to see in direct Monte Carlo simulations of the TASEP. We furthermore discuss in general terms scenarios that admit a distinction between static and dynamic phase behaviour.Comment: 27 pages, 18 figures. v2 to appear in J Phys A features minor corrections and better-quality figure

Slowest relaxation mode of the partially asymmetric exclusion process with open boundaries

We analyze the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process on a finite lattice and with the most general open boundary conditions. We extend results obtained recently for totally asymmetric diffusion [J. de Gier and F.H.L. Essler, J. Stat. Mech. P12011 (2006)] to the case of partial symmetry. We determine the finite-size scaling of the spectral gap, which characterizes the approach to stationarity at large times, in the low and high density regimes and on the coexistence line. We observe boundary induced crossovers and discuss possible interpretations of our results in terms of effective domain wall theories.Comment: 30 pages, 9 figures, typeset for pdflatex; revised versio

Exact Spectral Gaps of the Asymmetric Exclusion Process with Open Boundaries

We derive the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process with the most general open boundary conditions. By analysing these equations in detail for the cases of totally asymmetric and symmetric diffusion, we calculate the finite-size scaling of the spectral gap, which characterizes the approach to stationarity at large times. In the totally asymmetric case we observe boundary induced crossovers between massive, diffusive and KPZ scaling regimes. We further study higher excitations, and demonstrate the absence of oscillatory behaviour at large times on the ``coexistence line'', which separates the massive low and high density phases. In the maximum current phase, oscillations are present on the KPZ scale $t\propto L^{-3/2}$. While independent of the boundary parameters, the spectral gap as well as the oscillation frequency in the maximum current phase have different values compared to the totally asymmetric exclusion process with periodic boundary conditions. We discuss a possible interpretation of our results in terms of an effective domain wall theory.Comment: 42 pages, 25 figures; added appendix and minor correction

A polygenic risk score for multiple myeloma risk prediction

There is overwhelming epidemiologic evidence that the risk of multiple myeloma (MM) has a solid genetic background. Genome-wide association studies (GWAS) have identified 23 risk loci that contribute to the genetic susceptibility of MM, but have low individual penetrance. Combining the SNPs in a polygenic risk score (PRS) is a possible approach to improve their usefulness. Using 2361 MM cases and 1415 controls from the International Multiple Myeloma rESEarch (IMMEnSE) consortium, we computed a weighted and an unweighted PRS. We observed associations with MM risk with OR = 3.44, 95% CI 2.53–4.69, p = 3.55 × 10−15 for the highest vs. lowest quintile of the weighted score, and OR = 3.18, 95% CI 2.1 = 34–4.33, p = 1.62 × 10−13 for the highest vs. lowest quintile of the unweighted score. We found a convincing association of a PRS generated with 23 SNPs and risk of MM. Our work provides additional validation of previously discovered MM risk variants and of their combination into a PRS, which is a first step towards the use of genetics for risk stratification in the general population

Basal cell carcinoma of the vulva: a case report and systematic review of the literature

The vulva is an unusual site for basal cell carcinoma (BCC). Vulvar BCC accounts for <1% of all BCCs and <5% of all vulvar malignancies. We report the case of an 83 year‐old woman who presented with a 2‐month history of a tender labial growth, with histopathology confirming nodular BCC. We conducted a systematic literature review of the characteristics of reported cases of vulvar BCCs. A comprehensive systematic review of articles indexed for MEDLINE and Embase yielded 96 reports describing 437 patients with 446 BCCs of the vulva. The mean age at presentation was 70 (range 20–100). Most women had no underlying vulvar disease. Approximately 60% of cases were of the nodular subtype. Treatment approach varied widely with over half of cases treated with wide local or local excision. Mohs micrographic surgery (MMS) for vulvar BCC was first reported in 1988 with seven total MMS cases reported. Twenty‐three cases of recurrence have been reported; 21 of these cases after local excision but none following MMS. Vulvar BCC is a rarely reported cancer that affects older women predominantly. MMS represents a promising treatment for BCC in this anatomic location.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150570/1/ijd14307.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150570/2/ijd14307_am.pd

Expression quantitative trait loci of genes predicting outcome are associated with survival of multiple myeloma patients

Canadian Institutes of Health Research, Grant/ Award Number: 81274; Huntsman Cancer Institute Pilot Funds; Leukemia Lymphoma Society, Grant/Award Number: 6067-09; the National Institute of Health/National Cancer Institute, Grant/Award Numbers: P30 CA016672, P30 CA042014, P30 CA13148, P50 CA186781, R01 CA107476, R01 CA134674, R01 CA168762, R01 CA186646, R01 CA235026, R21 CA155951, R25 CA092049, R25 CA47888, U54 CA118948; Utah Population Database, Utah Cancer Registry, Huntsman Cancer Center Support Grant, Utah State Department of Health, University of Utah; VicHealth, Cancer Council Victoria, Australian National Health and Medical Research Council, Grant/Award Numbers: 1074383, 209057, 396414; Victorian Cancer Registry, Australian Institute of Health and Welfare, Australian National Death Index, Australian Cancer Database; Mayo Clinic Cancer Center; University of Pisa and DKFZThe authors thank all site investigators that contributed to the studies within the Multiple Myeloma Working Group (Interlymph Consortium), staff involved at each site and, most importantly, the study participants for their contributions that made our study possible. This work was partially supported by intramural funds of University of Pisa and DKFZ. This work was supported in part by the National Institute of Health/National Cancer Institute (R25 CA092049, P30 CA016672, R01 CA134674, P30 CA042014, R01 CA186646, R21 CA155951, U54 CA118948, P30 CA13148, R25 CA47888, R01 CA235026, R01 CA107476, R01 CA168762, P50 CA186781 and the NCI Intramural Research Program), Leukemia Lymphoma Society (6067-09), Huntsman Cancer Institute Pilot Funds, Utah PopulationDatabase, Utah Cancer Registry, Huntsman Cancer Center Support Grant, Utah StateDepartment of Health, University of Utah, Canadian Institutes of Health Research (Grant number 81274), VicHealth, Cancer Council Victoria, Australian National Health and Medical Research Council (Grants 209057, 396414, 1074383), Victorian Cancer Registry, Australian Institute of Health and Welfare, Australian National Death Index, Australian Cancer Database and the Mayo Clinic Cancer Center.Open Access funding enabled and organized by ProjektDEAL.The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.Gene expression profiling can be used for predicting survival in multiple myeloma (MM) and identifying patients who will benefit from particular types of therapy. Some germline single nucleotide polymorphisms (SNPs) act as expression quantitative trait loci (eQTLs) showing strong associations with gene expression levels. We performed an association study to test whether eQTLs of genes reported to be associated with prognosis of MM patients are directly associated with measures of adverse outcome. Using the genotype-tissue expression portal, we identified a total of 16 candidate genes with at least one eQTL SNP associated with their expression with P < 10(-7) either in EBV-transformed B-lymphocytes or whole blood. We genotyped the resulting 22 SNPs in 1327 MM cases from the International Multiple Myeloma rESEarch (IMMEnSE) consortium and examined their association with overall survival (OS) and progression-free survival (PFS), adjusting for age, sex, country of origin and disease stage. Three polymorphisms in two genes (TBRG4-rs1992292, TBRG4-rs2287535 and ENTPD1-rs2153913) showed associations with OS at P < .05, with the former two also associated with PFS. The associations of two polymorphisms in TBRG4 with OS were replicated in 1277 MM cases from the International Lymphoma Epidemiology (InterLymph) Consortium. A meta-analysis of the data from IMMEnSE and InterLymph (2579 cases) showed that TBRG4-rs1992292 is associated with OS (hazard ratio = 1.14, 95% confidence interval 1.04-1.26, P = .007). In conclusion, we found biologically a plausible association between a SNP in TBRG4 and OS of MM patients.Canadian Institutes of Health Research (CIHR) 81274Huntsman Cancer Institute Pilot FundsLeukemia and Lymphoma Society 6067-09United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH National Cancer Institute (NCI) P30 CA016672 P30 CA042014 P30 CA13148 P50 CA186781 R01 CA107476 R01 CA134674 R01 CA168762 R01 CA186646 R01 CA235026 R21 CA155951 R25 CA092049 R25 CA47888 U54 CA118948Utah Population Database, Utah Cancer Registry, Huntsman Cancer Center Support Grant, Utah State Department of Health, University of UtahVicHealth, Cancer Council Victoria, Australian National Health and Medical Research Council 1074383 209057 396414Victorian Cancer Registry, Australian Institute of Health and Welfare, Australian National Death Index, Australian Cancer DatabaseMayo Clinic Cancer CenterUniversity of PisaHelmholtz Associatio