categoryCompare, an analytical tool based on feature annotations

Assessment of high-throughput—omics data initially focuses on relative or raw levels of a particular feature, such as an expression value for a transcript, protein, or metabolite. At a second level, analyses of annotations including known or predicted functions and associations of each individual feature, attempt to distill biological context. Most currently available comparative- and meta-analyses methods are dependent on the availability of identical features across data sets, and concentrate on determining features that are differentially expressed across experiments, some of which may be considered “biomarkers.” The heterogeneity of measurement platforms and inherent variability of biological systems confounds the search for robust biomarkers indicative of a particular condition. In many instances, however, multiple data sets show involvement of common biological processes or signaling pathways, even though individual features are not commonly measured or differentially expressed between them. We developed a methodology, categoryCompare, for cross-platform and cross-sample comparison of high-throughput data at the annotation level. We assessed the utility of the approach using hypothetical data, as well as determining similarities and differences in the set of processes in two instances: (1) denervated skin vs. denervated muscle, and (2) colon from Crohn's disease vs. colon from ulcerative colitis (UC). The hypothetical data showed that in many cases comparing annotations gave superior results to comparing only at the gene level. Improved analytical results depended as well on the number of genes included in the annotation term, the amount of noise in relation to the number of genes expressing in unenriched annotation categories, and the specific method in which samples are combined. In the skin vs. muscle denervation comparison, the tissues demonstrated markedly different responses. The Crohn's vs. UC comparison showed gross similarities in inflammatory response in the two diseases, with particular processes specific to each disease

Rapid development of individual identification and presence systems for a critically endangered antelope, the Mountain bongo

Monitoring of species, particularly remnant populations requiring urgent conservation is often hampered by the lack of reliable tools for individual identification (using images or their spoor). Here, we develop rapid monitoring tools for individual animals of the Mountain bongo (Tragelaphus eurycerus isaaci), a critically endangered subspecies of the bongo only found in Kenya. We developed and tested an individual identification system using camera trap footage, as well as a quantitative tool to identify bongo spoor in the field, both useable by naïve observers. We implemented an information content approach to assess the importance of different visual elements in 61 individual bongos to optimise our identification system. We tested the reliability of the system with 15 naïve observers. We conclude that an optimal identification system should rely on three main visual features (stripe pattern, facial markings and horns appearance). We show that reliability amongst observers is high (κ = 0.64). We also developed a field scheme to identify footprint and spoor sign. Measurements of bongo footprints were compared with those of waterbuck (Kobus ellypsiprimnus), a syntopic antelope. Confusion occurs between spoor and footprints of both species. We find that differences in the aspect ratio of bongo and waterbuck footprints can identify the two species, 1.22 (±0.08) for bongo and 1.49 (±0.10) for waterbuck. The acquisition of reliable tools ensures monitoring activities are less dependent on individual expertise, which will allow consistent monitoring of bongo remnant populations in the future. The methods we used to develop these monitoring tools can help managers and field workers in the study of this and similar rare species where monitoring is a challenge

Parameterized optimized effective potential for atoms

The optimized effective potential equations for atoms have been solved by parameterizing the potential. The expansion is tailored to fulfill the known asymptotic behavior of the effective potential at both short and long distances. Both single configuration and multi configuration trial wave functions are implemented. Applications to several atomic systems are presented improving previous works. The results here obtained are very close to those calculated in either the Hartree-Fock and the multi configurational Hartree-Fock framework.Comment: 8 pages, 3 figure

The Color of Childhood: The Role of the Child/Human Binary in the Production of Anti-Black Racism

The binary between the figure of the child and the fully human being is invoked with regularity in analyses of race, yet its centrality to the conception of race has never been fully explored. For most commentators, the figure of the child operates as a metaphoric or rhetorical trope, a non-essential strategic tool in the perpetuation of White supremacy. As I show in the following, the child/human binary does not present a contingent or merely rhetorical construction but, rather, a central feature of racialization. Where Black peoples are situated as objects of violence it is often precisely because Blackness has been identified with childhood and childhood is historically identified as the archetypal site of naturalized violence and servitude. I proceed by offering a historical account of how Black peoples came to inherit the subordination and dehumanization of European childhood and how White youth were subsequently spared through their partial categorization as adults

Inconsistent boundaries

Research on this paper was supported by a grant from the Marsden Fund, Royal Society of New Zealand.Mereotopology is a theory of connected parts. The existence of boundaries, as parts of everyday objects, is basic to any such theory; but in classical mereotopology, there is a problem: if boundaries exist, then either distinct entities cannot be in contact, or else space is not topologically connected (Varzi in Noûs 31:26–58, 1997). In this paper we urge that this problem can be met with a paraconsistent mereotopology, and sketch the details of one such approach. The resulting theory focuses attention on the role of empty parts, in delivering a balanced and bounded metaphysics of naive space.PostprintPeer reviewe

Kinematics and hydrodynamics of spinning particles

In the first part (Sections 1 and 2) of this paper --starting from the Pauli current, in the ordinary tensorial language-- we obtain the decomposition of the non-relativistic field velocity into two orthogonal parts: (i) the "classical part, that is, the 3-velocity w = p/m OF the center-of-mass (CM), and (ii) the so-called "quantum" part, that is, the 3-velocity V of the motion IN the CM frame (namely, the internal "spin motion" or zitterbewegung). By inserting such a complete, composite expression of the velocity into the kinetic energy term of the non-relativistic classical (i.e., newtonian) lagrangian, we straightforwardly get the appearance of the so-called "quantum potential" associated, as it is known, with the Madelung fluid. This result carries further evidence that the quantum behaviour of micro-systems can be adirect consequence of the fundamental existence of spin. In the second part (Sections 3 and 4), we fix our attention on the total 3-velocity v = w + V, it being now necessary to pass to relativistic (classical) physics; and we show that the proper time entering the definition of the four-velocity v^mu for spinning particles has to be the proper time tau of the CM frame. Inserting the correct Lorentz factor into the definition of v^mu leads to completely new kinematical properties for v_mu v^mu. The important constraint p_mu v^mu = m, identically true for scalar particles, but just assumed a priori in all previous spinning particle theories, is herein derived in a self-consistent way.Comment: LaTeX file; needs kapproc.st

Solar System Processes Underlying Planetary Formation, Geodynamics, and the Georeactor

Only three processes, operant during the formation of the Solar System, are responsible for the diversity of matter in the Solar System and are directly responsible for planetary internal-structures, including planetocentric nuclear fission reactors, and for dynamical processes, including and especially, geodynamics. These processes are: (i) Low-pressure, low-temperature condensation from solar matter in the remote reaches of the Solar System or in the interstellar medium; (ii) High-pressure, high-temperature condensation from solar matter associated with planetary-formation by raining out from the interiors of giant-gaseous protoplanets, and; (iii) Stripping of the primordial volatile components from the inner portion of the Solar System by super-intense solar wind associated with T-Tauri phase mass-ejections, presumably during the thermonuclear ignition of the Sun. As described herein, these processes lead logically, in a causally related manner, to a coherent vision of planetary formation with profound implications including, but not limited to, (a) Earth formation as a giant gaseous Jupiter-like planet with vast amounts of stored energy of protoplanetary compression in its rock-plus-alloy kernel; (b) Removal of approximately 300 Earth-masses of primordial gases from the Earth, which began Earth's decompression process, making available the stored energy of protoplanetary compression for driving geodynamic processes, which I have described by the new whole-Earth decompression dynamics and which is responsible for emplacing heat at the mantle-crust-interface at the base of the crust through the process I have described, called mantle decompression thermal-tsunami; and, (c)Uranium accumulations at the planetary centers capable of self-sustained nuclear fission chain reactions.Comment: Invited paper for the Special Issue of Earth, Moon and Planets entitled Neutrino Geophysics Added final corrections for publicatio

Similar or Different? The Role of the Ventrolateral Prefrontal Cortex in Similarity Detection

Patients with frontal lobe syndrome can exhibit two types of abnormal behaviour when asked to place a banana and an orange in a single category: some patients categorize them at a concrete level (e.g., “both have peel”), while others continue to look for differences between these objects (e.g., “one is yellow, the other is orange”). These observations raise the question of whether abstraction and similarity detection are distinct processes involved in abstract categorization, and that depend on separate areas of the prefrontal cortex (PFC). We designed an original experimental paradigm for a functional magnetic resonance imaging (fMRI) study involving healthy subjects, confirming the existence of two distinct processes relying on different prefrontal areas, and thus explaining the behavioural dissociation in frontal lesion patients. We showed that: 1) Similarity detection involves the anterior ventrolateral PFC bilaterally with a right-left asymmetry: the right anterior ventrolateral PFC is only engaged in detecting physical similarities; 2) Abstraction per se activates the left dorsolateral PFC