Relative Comparison Kernel Learning with Auxiliary Kernels

In this work we consider the problem of learning a positive semidefinite kernel matrix from relative comparisons of the form: "object A is more similar to object B than it is to C", where comparisons are given by humans. Existing solutions to this problem assume many comparisons are provided to learn a high quality kernel. However, this can be considered unrealistic for many real-world tasks since relative assessments require human input, which is often costly or difficult to obtain. Because of this, only a limited number of these comparisons may be provided. In this work, we explore methods for aiding the process of learning a kernel with the help of auxiliary kernels built from more easily extractable information regarding the relationships among objects. We propose a new kernel learning approach in which the target kernel is defined as a conic combination of auxiliary kernels and a kernel whose elements are learned directly. We formulate a convex optimization to solve for this target kernel that adds only minor overhead to methods that use no auxiliary information. Empirical results show that in the presence of few training relative comparisons, our method can learn kernels that generalize to more out-of-sample comparisons than methods that do not utilize auxiliary information, as well as similar methods that learn metrics over objects

Bottlenose dolphin (Tursiops truncatus) strandings in South Carolina, 1992–1996

From 1992 to 1996, 153 bottlenose dolphin stranded in South Carolina, accounting for 73% of all marine mammal strandings during this period. The objectives of our study were to evaluate data from these strandings to deter-mine 1) annual trends in strandings, 2) seasonal and spatial distribution trends, 3) life history parameters such as sex ratio and age classes, 3) seasonal trends in reproduction, and 4) the extent to which humans have played a role in causing these strandings (human inter-actions). The results showed that 49% of the bottlenose dolphin strandings occurred between April and July; the greatest number of strandings occurred in July (n=22). There was a significant seasonal increase in the distribution of bottlenose dolphin strandings in the northern portion of the state from November to March. Bottlenose dolphin neonates stranded in every month of the year, except March and October, and represented 19.6% of the total number of strandings with known length (n=138). Fifty-five percent (n=15) of bottlenose dolphin neonatal strandings occurred between May and July. Bottlenose dolphins determined to have died as the result of human interaction accounted for 23.1% of the total number of bottlenose dolphin strandings (excluding those for which a determination could not be made).Incidents of bottlenose dolphin entanglements in nets accounted for 16 of these cases

Maze solvers demystified and some other thoughts

There is a growing interest towards implementation of maze solving in spatially-extended physical, chemical and living systems. Several reports of prototypes attracted great publicity, e.g. maze solving with slime mould and epithelial cells, maze navigating droplets. We show that most prototypes utilise one of two phenomena: a shortest path in a maze is a path of the least resistance for fluid and current flow, and a shortest path is a path of the steepest gradient of chemoattractants. We discuss that substrates with so-called maze-solving capabilities simply trace flow currents or chemical diffusion gradients. We illustrate our thoughts with a model of flow and experiments with slime mould. The chapter ends with a discussion of experiments on maze solving with plant roots and leeches which show limitations of the chemical diffusion maze-solving approach.Comment: This is a preliminary version of the chapter to be published in Adamatzky A. (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Transcriptomic data of bovine ovarian granulosa cells of control and High A4 cows

Microarray analysis using Affymetrix Bovine GeneChip 1.0 ST Array to determine RNA expression analysis was performed on somatic granulosa cells from two different groups of cows classified based on androstenedione concentration within the follicular fluid (Control vs High A4) of estrogen-active dominant follicles. The normalized linear microarray data was deposited to the NCBI GEO repository (GSE97017 - RNA Expression Data from Bovine Ovarian Granulosa Cells from High or Low Androgen-Content Follicles). Subsequent ANOVA determined genes that were enriched (≥ 1.5 fold more) or decreased (≤ 1.5 fold less) in the High A4 granulosa cells compared to Control granulosa cells and analyzed filtered datasets of these differentially expressed genes are presented as tables. MicroRNAs that are differentially expressed in Control and High A4 granulosa cells are also reported in tables. The standard deviation of the analyzed array data in relation to the log of the expression values are shown as a figure. Ingenuity Pathway Analysis determined upstream regulators of differently expressed genes as presented in a table. These data have been further analyzed and interpreted in the companion article “A High-Androgen Microenvironment Inhibits Granulosa Cell Proliferation and Alters Cell Identity.

Surface acoustic wave attenuation by a two-dimensional electron gas in a strong magnetic field

The propagation of a surface acoustic wave (SAW) on GaAs/AlGaAs heterostructures is studied in the case where the two-dimensional electron gas (2DEG) is subject to a strong magnetic field and a smooth random potential with correlation length Lambda and amplitude Delta. The electron wave functions are described in a quasiclassical picture using results of percolation theory for two-dimensional systems. In accordance with the experimental situation, Lambda is assumed to be much smaller than the sound wavelength 2*pi/q. This restricts the absorption of surface phonons at a filling factor \bar{\nu} approx 1/2 to electrons occupying extended trajectories of fractal structure. Both piezoelectric and deformation potential interactions of surface acoustic phonons with electrons are considered and the corresponding interaction vertices are derived. These vertices are found to differ from those valid for three-dimensional bulk phonon systems with respect to the phonon wave vector dependence. We derive the appropriate dielectric function varepsilon(omega,q) to describe the effect of screening on the electron-phonon coupling. In the low temperature, high frequency regime T << Delta (omega_q*Lambda /v_D)^{alpha/2/nu}, where omega_q is the SAW frequency and v_D is the electron drift velocity, both the attenuation coefficient Gamma and varepsilon(omega,q) are independent of temperature. The classical percolation indices give alpha/2/nu=3/7. The width of the region where a strong absorption of the SAW occurs is found to be given by the scaling law |Delta \bar{\nu}| approx (omega_q*Lambda/v_D)^{alpha/2/nu}. The dependence of the electron-phonon coupling and the screening due to the 2DEG on the filling factor leads to a double-peak structure for Gamma(\bar{\nu}).Comment: 17 pages, 3 Postscript figures, minor changes mad

Identification of Lipids and Cytokines in Plasma and Follicular Fluid before and after Follicle-Stimulating Hormone Stimulation as Potential Markers for Follicular Maturation in Cattle

The process of follicle maturation leading to ovulation is a key milestone in female fertility. It is known that circulating lipids and cytokines play a role in the follicle’s ability to go through follicular maturation and the ovulatory processes. However, the specific mechanisms are not well understood. We posit that dysregulation of granulosa cells influences the ovarian environment, which tries to adapt by changing released lipids and cytokines to achieve follicular maturation. Eleven non-lactating adult females underwent estrus synchronization with two injections of PGF2 14 days apart. Daily blood samples were collected for 28 days to monitor steroid hormone production after the second injection. To understand the potential impacts of lipids and cytokines during ovulation, a low-dose FSH stimulation (FSHLow) was performed after resynchronization of cows, and daily blood samples were collected for 14 days to monitor steroid hormone production until ovariectomies. The lipidomic analysis demonstrated increased circulating diacylglycerides and triacylglycerides during the mid-luteal phase and after FSHLow treatment. Cholesteryl esters decreased in circulation but increased in follicular fluid (FF) after FSHLow. Increased circulating concentrations of TNF and reduced CXCL9 were observed in response to FSHLow. Therefore, specific circulating lipids and cytokines may serve as markers of normal follicle maturation

Vascular Endothelial Growth Factor A 165 rescues steroids, inflammation and follicle arrest in High Androstenedione cows

A population of cows with excess androstenedione (A4; High A4) in follicular fluid, with follicular arrest, granulosa cell dysfunction, and a 17% reduction in calving rate was previously identified. We hypothesized that excess A4 in the ovarian microenvironment caused the follicular arrest in High A4 cows and that vascular endothelial growth factor A would rescue the High A4 phenotype. In trial 1, prior to culture, High A4 ovarian cortex (n=9) had greater numbers of early stage follicles (primordial) and fewer later-stage follicles compared to controls (n=11). Culture for 7 days did not relieve this follicular arrest; instead, High A4 ovarian cortex had increased indicators of inflammation, anti-Mullerian hormone, and A4 secretion compared to controls. In trial 2, we tested if vascular endothelial growth factor A (VEGFA) angiogenic (165) and antiangiogenic (VEGFA165b) isoforms could rescue the High A4 phenotype. High A4 (n=5) and control (n=5) ovarian cortex was cultured with (1) PBS, (2) VEGFA165 (50 ng/mL), (3) VEGFA165b (50 ng/mL), or (4) VEGFA165+VEGFA165b (50 ng/mL each) for 7 days. Follicular progression increased with VEGFA165 in High A4 cows with greater early primary, primary, and secondary follicles than controls. Similar to trial 1, High A4 ovarian cortex secreted greater concentrations of A4 and other steroids and had greater indicators of inflammation compared to controls. However, VEGFA165 rescued steroidogenesis, oxidative stress, and fibrosis. Both VEGFA isoforms reduced specific pro-inflammatory cytokines in High A4 cows to control levels. Thus, VEGFA165 may be a potential therapeutic to restore the ovarian steroidogenic microenvironment to promote folliculogenesis

An Exploratory Study into Objective and Reported Characteristics of Neuropathic Pain in Women with Chronic Pelvic Pain

Chronic pelvic pain (CPP) affects 5.7-26.6% women worldwide. 55% have no obvious pathology and 40% have associated endometriosis. Neuropathic pain (NeP) is pain arising as a consequence of a lesion/disease affecting the somatosensory system. The prevalence of NeP in women with CPP is not known. The diagnosis of NeP is challenging because there is no gold-standard assessment. Questionnaires have been used in the clinical setting to diagnose NeP in other chronic pain conditions and quantitative sensory testing (QST) has been used in a research setting to identify abnormal sensory function. We aimed to determine if women with chronic pelvic pain (CPP) have a neuropathic pain (NeP) component to their painful symptoms and how this is best assessed. We performed an exploratory prospective cohort study of 72 pre-menopausal women with a diagnosis of CPP. They underwent a clinician completed questionnaire (DN4) and completed the S-LANSS and PainDETECT™ questionnaires. Additionally QST testing was performed by a clinician. They also completed a patient acceptability questionnaire. Clinical features of NeP were identified by both questionnaires and QST. Of the women who were NeP positive, 56%, 35% and 26% were identified by the S-LANSS, DN4 and PainDETECT™ respectively. When NeP was identified by questionnaire, the associated laparoscopy findings were similar irrespective of which questionnaire was used. No subject had entirely unchanged QST parameters. There were distinct loss and gain subgroups, as well as mixed alteration in function, but this was not necessarily clinically significant in all patients. 80% of patients were confident that questionnaires could diagnose NeP, and 90% found them easy to complete. Early identification of NeP in women with CPP with a simple questionnaire could facilitate targeted therapy with neuromodulators, which are cheap, readily available, and have good safety profiles. This approach could prevent unnecessary or fertility-compromising surgery and prolonged treatment with hormones