Metadata Service to Enable Display of Rich Artifacts in Machine Learning Pipelines

Cloud-based machine learning (ML) platforms enable ML practitioners to build, rebuild, and serve multiple machine learning models in production environments. Proper ML metadata tracking and management is important to enable large-scale experimentation and to provide traceability and verifiability for modern production ML. This disclosure describes a ML metadata service to manage the lifecycle of metadata consumed and produced by ML pipelines. The ML metadata service enables logging detailed metadata as artifacts, capturing metadata as typed artifacts, and capturing a ML pipeline in an intuitive workflow graph. The metadata service enables provision of a ML dashboard that displays visualizations of a ML workflow along with the relevant metadata for each type of entity and supports queries for models and/or datasets that meet specific criteria

Efficient Bayesian-based Multi-View Deconvolution

Light sheet fluorescence microscopy is able to image large specimen with high resolution by imaging the sam- ples from multiple angles. Multi-view deconvolution can significantly improve the resolution and contrast of the images, but its application has been limited due to the large size of the datasets. Here we present a Bayesian- based derivation of multi-view deconvolution that drastically improves the convergence time and provide a fast implementation utilizing graphics hardware.Comment: 48 pages, 20 figures, 1 table, under review at Nature Method

Impact of cognitive stimulation on ripples within human epileptic and non-epileptic hippocampus

Background: Until now there has been no way of distinguishing between physiological and epileptic hippocampal ripples in intracranial recordings. In the present study we addressed this by investigating the effect of cognitive stimulation on interictal high frequency oscillations in the ripple range (80-250 Hz) within epileptic (EH) and non-epileptic hippocampus (NH). Methods: We analyzed depth EEG recordings in 10 patients with intractable epilepsy, in whom hippocampal activity was recorded initially during quiet wakefulness and subsequently during a simple cognitive task. Using automated detection of ripples based on amplitude of the power envelope, we analyzed ripple rate (RR) in the cognitive and resting period, within EH and NH. Results: Compared to quiet wakefulness we observed a significant reduction of RR during cognitive stimulation in EH, while it remained statistically marginal in NH. Further, we investigated the direct impact of cognitive stimuli on ripples (i.e. immediately post-stimulus), which showed a transient statistically significant suppression of ripples in the first second after stimuli onset in NH only. Conclusion: Our results point to a differential reactivity of ripples within EH and NH to cognitive stimulation

Search for CP violation in D+→ϕπ+ and D+s→K0Sπ+ decays

A search for CP violation in D + → ϕπ + decays is performed using data collected in 2011 by the LHCb experiment corresponding to an integrated luminosity of 1.0 fb−1 at a centre of mass energy of 7 TeV. The CP -violating asymmetry is measured to be (−0.04 ± 0.14 ± 0.14)% for candidates with K − K + mass within 20 MeV/c 2 of the ϕ meson mass. A search for a CP -violating asymmetry that varies across the ϕ mass region of the D + → K − K + π + Dalitz plot is also performed, and no evidence for CP violation is found. In addition, the CP asymmetry in the D+s→K0Sπ+ decay is measured to be (0.61 ± 0.83 ± 0.14)%

eIF5A Promotes Translation Elongation, Polysome Disassembly and Stress Granule Assembly

Stress granules (SGs) are cytoplasmic foci at which untranslated mRNAs accumulate in cells exposed to environmental stress. We have identified ornithine decarboxylase (ODC), an enzyme required for polyamine synthesis, and eIF5A, a polyamine (hypusine)-modified translation factor, as proteins required for arsenite-induced SG assembly. Knockdown of deoxyhypusine synthase (DHS) or treatment with a deoxyhypusine synthase inhibitor (GC7) prevents hypusine modification of eIF5A as well as arsenite-induced polysome disassembly and stress granule assembly. Time-course analysis reveals that this is due to a slowing of stress-induced ribosome run-off in cells lacking hypusine-eIF5A. Whereas eIF5A only marginally affects protein synthesis under normal conditions, it is required for the rapid onset of stress-induced translational repression. Our results reveal that hypusine-eIF5A-facilitated translation elongation promotes arsenite-induced polysome disassembly and stress granule assembly in cells subjected to adverse environmental conditions

Representing and comparing protein structures as paths in three-dimensional space

BACKGROUND: Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction. RESULTS: We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure. CONCLUSION: Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver

Light Perception in Two Strictly Subterranean Rodents: Life in the Dark or Blue?

BACKGROUND: The African mole-rats (Bathyergidae, Rodentia) are strictly subterranean, congenitally microphthalmic rodents that are hardly ever exposed to environmental light. Because of the lack of an overt behavioural reaction to light, they have long been considered to be blind. However, recent anatomical studies have suggested retention of basic visual capabilities. In this study, we employed behavioural tests to find out if two mole-rat species are able to discriminate between light and dark, if they are able to discriminate colours and, finally, if the presence of light in burrows provokes plugging behaviour, which is assumed to have a primarily anti-predatory function. METHODOLOGY/PRINCIPAL FINDING: We used a binary choice test to show that the silvery mole-rat Heliophobius argenteocinereus and the giant mole-rat Fukomys mechowii exhibit a clear photoavoidance response to full-spectrum ("white"), blue and green-yellow light, but no significant reaction to ultraviolet or red light during nest building. The mole-rats thus retain dark/light discrimination capabilities and a capacity to perceive short to medium-wavelength light in the photopic range of intensities. These findings further suggest that the mole-rat S opsin has its absorption maximum in the violet/blue part of the spectrum. The assay did not yield conclusive evidence regarding colour discrimination. To test the putative role of vision in bathyergid anti-predatory behaviour, we examined the reaction of mole-rats to the incidence of light in an artificial burrow system. The presence of light in the burrow effectively induced plugging of the illuminated tunnel. CONCLUSION/SIGNIFICANCE: Our findings suggest that the photopic vision is conserved and that low acuity residual vision plays an important role in predator avoidance and tunnel maintenance in the African mole-rats

Variation in Phenotype, Parasite Load and Male Competitive Ability across a Cryptic Hybrid Zone

BackgroundMolecular genetic studies are revealing an increasing number of cryptic lineages or species, which are highly genetically divergent but apparently cannot be distinguished morphologically. This observation gives rise to three important questions: 1) have these cryptic lineages diverged in phenotypic traits that may not be obvious to humans; 2) when cryptic lineages come into secondary contact, what are the evolutionary consequences: stable co-existence, replacement, admixture or differentiation and 3) what processes influence the evolutionary dynamics of these secondary contact zones?Methodology/principal findingsTo address these questions, we first tested whether males of the Iberian lizard Lacerta schreiberi from two highly genetically divergent, yet morphologically cryptic lineages on either side of an east-west secondary contact could be differentiated based on detailed analysis of morphology, coloration and parasite load. Next, we tested whether these differences could be driven by pre-copulatory intra-sexual selection (male-male competition). Compared to eastern males, western males had fewer parasites, were in better body condition and were more intensely coloured. Although subtle environmental variation across the hybrid zone could explain the differences in parasite load and body condition, these were uncorrelated with colour expression, suggesting that the differences in coloration reflect heritable divergence. The lineages did not differ in their aggressive behaviour or competitive ability. However, body size, which predicted male aggressiveness, was positively correlated with the colour traits that differed between genetic backgrounds.Conclusions/significanceOur study confirms that these cryptic lineages differ in several aspects that are likely to influence fitness. Although there were no clear differences in male competitive ability, our results suggest a potential indirect role for intra-sexual selection. Specifically, if lizards use the colour traits that differ between genetic backgrounds to assess the size of potential rivals or mates, the resulting fitness differential favouring western males could result in net male-mediated gene flow from west to east across the current hybrid zone.Devi Stuart-Fox, Raquel Godinho, Joëlle Goüy de Bellocq, Nancy R. Irwin, José Carlos Brito, Adnan Moussalli, Pavel Široký, Andrew F. Hugall and Stuart J. E. Bair

Rutas tróficas en macrozooplancton del Lago de Tota - Boyacá, Colombia

1 recurso en línea (56 páginas) : ilustraciones, figuras, tablas.In aquatic ecosystems inputs of matter and energy present in greater or lesser extent depending on the basin, given the origin and quality of these resources, you can alter the balance in metabolism or interactions in the food web. Using stable isotopes of carbon and nitrogen, the link between potential sources of funds and use established by macrozooplankton species in Lake Big and Lake Fellow the Lake Tota sectors. Trophic possible ways the role of each species in the proposed network, as well. In general, most of this study, most species have a bond with the autotrophic pathway, being the phytoplankton the food resource base for the food web, commonly found impoverished carbon signals. Particularly, the analysis showed a variation in the source or resource for two species (Daphnia laevis and Bosmina (Bosmina) cf. longirostris), with an enrichment in its signal to 19.92 ‰ -20.34 ‰ δ13C, which can be given by plasticity in their food supply, and even if Boeckella gracilis having a signal indicating a specialization in its appeal with carbon impoverished -30 to -26 ‰ values δ13C while nitrogen values are enriched with an average value 20.21 ‰ in δ15N. To set the trophic fractionation means establishing three groups, the first (herbivores) consisting of (D. laevis, B. (Bosmina) and Ceriodaphnia pulchella cf. longirostris), the second (omnivore) which is (Daphnia pulex, Macrocyclops sp. and Cyclopoida), and a third group (secondary consumer) where is the only calanoido B. gracilis. In comparing the temporal variation is observed that there is a significant change in signals δ13C and δ15N of some species in relation to the influence of sources and allochthonous or autochthonous origin, spatial variation was not significant. It is concluded that the macrozooplanton Lake Tota, has a strong link with the autotrophic pathway and pelagic trophic levels have 3 sections, plus the primary producers and the food web in general tends to have an amplitude of trophic niche.En los ecosistemas acuáticos se presentan aportes de materia y energía, en mayor o menor proporción dependiendo de su cuenca, dado el origen y calidad de estos recursos, se puede alterar el balance en el metabolismo o las interacciones en la red trófica. Utilizando los isotopos estables de Carbono y Nitrógeno, se estableció el vínculo entre fuentes potenciales de recursos y el uso por las especies del macrozooplancton en los sectores Lago grande y Lago chico del lago de Tota (Boyacá). Así, se propusieron las posibles vías tróficas y el rol de cada especie en la red. En general, en la mayor parte de este estudio, las especies tuvieron un vínculo marcado con la vía autotrófica, siendo el fitoplancton el recurso alimenticio base para la red trófica, encontrando comúnmente señales empobrecidas de carbono. Particularmente, el análisis mostró una variación en la fuente o recurso para dos especies (Daphnia laevis y Bosmina (Bosmina) cf. longirostris), con un enriquecimiento en su señal de 19.92‰ δ13C a -20.34‰ δ13C, lo que se puede dar por una plasticidad en su fuente alimenticia, e incluso el caso de Boeckella gracilis que tiene una señal que indica una especialización en su recurso con valores empobrecidos de carbono -30 a -26‰ δ13C mientras que los valores de nitrógeno son enriquecidos con un valor promedio de 20.21‰ en δ15N. Para establecer el fraccionamiento trófico medio se formaron tres grupos, el primero (herbívoros) conformado por (D. laevis, B. (Bosmina) cf. longirostris y Ceriodaphnia pulchella), el segundo (omnívoro) en el que se encuentra (Daphnia pulex, Macrocyclops sp. y Cyclopoida), y un tercer grupo (Consumidor secundario) donde esta B. gracilis el único calanoido. En la comparación de la variación temporal, se observa que hay un cambio significativo en las señales de δ13C y δ15N de algunas especies en relación a la influencia de las fuentes y su origen alóctono o autóctono, la variación espacial no fue significativa. Se concluye que el macrozooplanton del lago de Tota, tiene un fuerte vínculo con la vía autotrófica y que los niveles tróficos pelágicos tienen 3 eslabones, más los productores primarios, y la red trófica en general tiende a tener una amplitud del nicho trófico. En los ecosistemas acuáticos se presentan aportes de materia y energía, en mayor o menor proporción dependiendo de su cuenca, dado el origen y calidad de estos recursos, se puede alterar el balance en el metabolismo o las interacciones en la red trófica. Utilizando los isotopos estables de Carbono y Nitrógeno, se estableció el vínculo entre fuentes potenciales de recursos y el uso por las especies del macrozooplancton en los sectores Lago grande y Lago chico del lago de Tota (Boyacá). Así, se propusieron las posibles vías tróficas y el rol de cada especie en la red. En general, en la mayor parte de este estudio, las especies tuvieron un vínculo marcado con la vía autotrófica, siendo el fitoplancton el recurso alimenticio base para la red trófica, encontrando comúnmente señales empobrecidas de carbono. Particularmente, el análisis mostró una variación en la fuente o recurso para dos especies (Daphnia laevis y Bosmina (Bosmina) cf. longirostris), con un enriquecimiento en su señal de 19.92‰ δ13C a -20.34‰ δ13C, lo que se puede dar por una plasticidad en su fuente alimenticia, e incluso el caso de Boeckella gracilis que tiene una señal que indica una especialización en su recurso con valores empobrecidos de carbono -30 a -26‰ δ13C mientras que los valores de nitrógeno son enriquecidos con un valor promedio de 20.21‰ en δ15N. Para establecer el fraccionamiento trófico medio se formaron tres grupos, el primero (herbívoros) conformado por (D. laevis, B. (Bosmina) cf. longirostris y Ceriodaphnia pulchella), el segundo (omnívoro) en el que se encuentra (Daphnia pulex, Macrocyclops sp. y Cyclopoida), y un tercer grupo (Consumidor secundario) donde esta B. gracilis el único calanoido. En la comparación de la variación temporal, se observa que hay un cambio significativo en las señales de δ13C y δ15N de algunas especies en relación a la influencia de las fuentes y su origen alóctono o autóctono, la variación espacial no fue significativa. Se concluye que el macrozooplanton del lago de Tota, tiene un fuerte vínculo con la vía autotrófica y que los niveles tróficos pelágicos tienen 3 eslabones, más los productores primarios, y la red trófica en general tiende a tener una amplitud del nicho trófico.Bibliografía: páginas 46-56.MaestríaMagíster en Ciencias Biológica