Miracle-dz/UniFAR-FTUs huggingface dataset:
Title: Detecting object boundaries in natural images requires ‘incitatory’ cell-cell interactions

: Detecting object boundaries is crucial for recognition, but how the process unfolds in visual cortex remains unknown. To study the problem faced by a hypothetical boundary cell (BC), and to predict how cortical circuitry could produce a BC from a population of conventional “simple cells” (SCs), we labeled 30,000 natural image patches and used Bayes’ rule to determine how an SC should affect a BC depending on its offset in receptive field position and orientation. We identified three types of cell-cell interactions: monotonic excitatory and inhibitory, with various thresholds, slopes, and amplitudes, and a spectrum of non-monotonic (U-shaped) interactions. Using simple models we show a common cortical circuit motif consisting of monosynaptic excitation and disynaptic inhibition – an arrangement we call "incitation" – can produce the entire spectrum of SC-BC interactions found in our dataset. Moreover, we show that the synaptic weights that parameterize the incitation circuit can be learned by a simple (1-layer) gradient descent learning rule. We conclude that trainable incitatory interconnections may be a general computational mechanism used by the cortex to help solve difficult natural classification problems. (300 cells (2) we show that the systematically on relative and and come in a variety of forms including monotonic excitation and inhibition and various bump-shaped functions; (3) we show that a mixed excitatory-inhibitory, or “incitatory”, circuit motif that is known to exist in V1 is capable of producing the entire spectrum of simple cell–boundary cell interactions that we catalogued, and (4) we show that the synaptic weights that parameterize the incitation circuit can be learned by one of the simplest known developmental/plasticity rules: a 1-layer “delta” rule.
WEB Treatment of Intracranial Aneurysms: Feasibility, Complications, and 1-Month Safety Results with the WEB DL and WEB SL/SLS in the French Observatory

BACKGROUND AND PURPOSE: Safety analyses in the French Observatory have shown that treatment of intracranial aneurysms by using flow disruption with the Woven EndoBridge Device (WEB) is safe, with low morbidity and no mortality. The objective of this study was to analyze treatment feasibility, complications, and safety results in patients treated with the Woven EndoBridge Device Dual-Layer (WEB DL) and Woven EndoBridge Device Single-Layer/Single-Layer Sphere (WEB SL/SLS) in the French Observatory. MATERIALS AND METHODS: Patients with bifurcation aneurysms were included in this prospective, multicenter good clinical practices study. A medical monitor independently analyzed procedural and clinical data. The study started with the WEB DL, and secondarily, the WEB SL/SLS was authorized in the study. RESULTS: Between November 2012 and January 2014, 10 French centers included 62 patients with 63 aneurysms. Thirty patients with 31 aneurysms were treated with the WEB DL, and 32 patients with 32 aneurysms, with the WEB SL/SLS. The percentage of anterior communicating artery aneurysms treated with WEB SL/SLS was significantly higher (37.5%) compared with WEB DL (12.9%) (P = .04). The WEB SL/SLS was more frequently used in aneurysms of <10 mm than the WEB DL (respectively, 96.9% and 67.7%; P = .002). Morbidity was similar in both groups (WEB DL, 3.3%; WEB SL/SLS, 3.1%), and mortality was 0.0% in both groups. CONCLUSIONS: This comparative study shows increased use of WEB treatment in ruptured, small, and anterior communicating artery aneurysms when using WEB SL/SLS. There was a trend toward fewer thromboembolic complications with the WEB SL/SLS. With both the WEB DL and WEB SL/SLS, the treatment was safe, with low morbidity and no mortality.
Coordinated Machine Learning and Decision Support for Situation Awareness.

For applications such as force protection, an effective decision maker needs to maintain an unambiguous grasp of the environment. Opportunities exist to leverage computational mechanisms for the adaptive fusion of diverse information sources. The current research employs neural networks and Markov chains to process information from sources including sensors, weather data, and law enforcement. Furthermore, the system operator’s input is used as a point of reference for the machine learning algorithms. More detailed features of the approach are provided, along with an example force protection scenario. SAND2007-6058 Unlimited Release Printed September 2007
Multiple energy-dispersed ion precipitations in the low-latitude auroral oval: Evidence of E × B drift effect and upward flowing ion contribution

The polar-orbiting satellites, Akebono and DMSP F8, have frequently observed energy-dispersed ion precipitation events in the low-latitude auroral oval. The general properties of these precipitations are the following: (1) the characteristic energy decreases with decreasing latitude, (2) the signatures appear simultaneously with the diffuse components of electrons and ions on closed field lines, and (3) multiple (overlapped) signatures of the energy-dispersed ion precipitations are sometimes observed simultaneously in the northern and the southern hemispheres. These precipitation events are classified into two types: type A and type B according to their energy ratios and mass composition. The ratios between the energies of the type A multiple energy-dispersed signatures are constants 1:32:52:72 or 1:22 (“odd” or “natural” integer cases). These odd or natural integers indicate the ratios of the flight distances from the source region to the observation point of ion clusters consisting mainly of a single ion species. There are two possible sources: upward flowing ions (UFIs) from the ionosphere and bidirectional ion injection in the equatorial region. The latter model, however, is consistent only with the odd-integer case. The triple energy-dispersed signatures (type B) consist of three ion species (H+, He+, O+), and the ratios of the energies of these signatures always correspond to the mass ratios; that is, E(H+):E(He+):E(O+) = M(H+);M(He+):M(O+) = 1:4:16. This relationship indicates that these multicomposition ion clusters of ionospheric origin have the same flow velocity and the source distance. We conclude that the source of these two types of the energy-dispersed ion precipitations are UFIs ejected from the ionosphere, The ions of UFI origin are velocity-filtered (energy-dispersed), dominated by the E × B drift on closed field lines, and reenter the ionosphere as downward flowing ions. The pitch angle distributions indicate that parallel acceleration through an electrostatic potential producing the UFI beams is the most probable acceleration process.
Higher Criticism Thresholding: Optimal Feature Selection when Useful Features

Motivated by many ambitious modern applications – genomics and proteomics are examples, we consider a two-class linear classification in high-dimensional, low-sample size setting (a.k.a. p n). We consider the case where among a large number of features (dimensions), only a small fraction of them is useful. The useful features are unknown to us, and each of them contributes weakly to the classification decision – we call this setting the rare/weak model (RW Model [2]). The success of linear classification hinges on how to select a small subset of useful features.
Journal Pre-proof Mapping cyto- and receptor architectonics to understand brain function and connectivity

This review focuses on cyto- and receptor architectonics as biological correlates of function and connectivity. It introduces the three-dimensional cytoarchitectonic probabilistic maps of cortical areas and nuclei of Julich-Brain Atlas, available at EBRAINS, to study structure-functions relationships. The maps are linked to the BigBrain as microanatomical reference model and template space. The siibra software tool suite enables a programmatic access to the maps and to receptorarchitectonic data that are anchored to the brain areas. Such cellular and molecular data are tools for studying MR-connectivity including modeling and simulation. At the end we highlight perspectives of the Julich-Brain, as well as methodological considerations. Thus, microstructural maps as part of a multimodal atlas enable one to elucidate the biological correlates of large-scale networks and brain function with high anatomical detail, which provides a basis to study brains of patients with psychiatric disorders.
Height-Latitude Structure of Planetary Waves in the Stratosphere and Troposphere

When constructing empirical models of middle atmosphere (CIRA-72, CIRA-86) the main attention is focused on zonal-averaged fields of wind, temperature and geopotehtial and also on annual and semiannual harmonics of these parameters. Last decade thanks to (owing to) efforts Middle Atmosphere Group at the UK Meteorological Office global grid data of mentioned parameters up to the altitudes of upper stratosphere have emerged. These data allow one to construct empirical model of stratosphere with three-dimensional resolution. In particular, using Fourier analysis, one may investigate three-dimensional spatial structure of thermodynamical fields. In present paper from BADC UKMO stratospheric assimilated data for the Northern and Southern Hemisphere period of 1992-2002 for the altitude region from 1000 to 0.316 Hpa amplitudes, phases and a contribution to dispersion of zonal and geopotehtial, zonal and meridional wind for wave number 1 and 2 were calculated. Month mean (1992-2002) fields of meteorological elements were used. Such procedure leads to smoothing of all time oscillations with the period less than 30 days. Because of this obtained amplitudes and phases characterize such large-scale wave processes, which may be considered as stationary. It is in this meaning that we shall further use the term stationary planetary waves.
Diet and metabolic state are the main factors determining 1 concentrations of perfluoroalkyl substances in female polar bears 2 from Svalbard 3

Sabrina Tartu; Sophie Bourgeon; Jon Aars; Magnus Andersen; Karen Lone; Bjørn 4 Munro Jenssen; Anuschka Polder; Gregory W. Thiemann; Vidar Torget; Jeffrey M. 5 Welker and Heli Routti 6 1 Norwegian Polar Institute, Fram Centre, Tromsø, Norway 7 2 UiT-The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, 8 Norway 9 3 Norwegian University of Science and Technology, Department of Biology, Trondheim, 10 Norway 11 4 Norwegian University of Life Science, Campus Adamstua, Oslo, Norway 12 5 York University, Faculty of Environmental Studies, Toronto, ON, Canada 13 6 University of Alaska Anchorage, Department of Biological Sciences, Anchorage, AK, USA 14 7 University Center in Svalbard, Longyearbyen, Svalbard, Norway 15
Signal strength and climate relationships in 13C/12C ratios of tree ring cellulose from oak in east England

Annual oak (Quercus robur L.) latewood δ 13 C values are presented for the period 1895-1994 from two sites with different hydrological characteristics. Both ring width and δ 13 C indices record high-frequency common forcing better than lower-frequency forcing. At both sites the high-frequency variance in the δ 13 C indices of latewood cellulose is highly correlated with combined July and August environmental variables. The association between the high-frequency variance in annual ring width indices and climate is not as strong. Higher correlations with environmental variables were found for the high-frequency δ 13 C indices at the dry site (Sandringham) than at the wet site (Babingley), but the differences are not statistically significant. These results illustrate the need for routine signal quantification in isotope records and hence a requirement for between-tree replication of isotope series in future studies. High-frequency (year-to-year) interseries correlation is shown to be relatively strong, indicating that only small numbers of replicate series are needed to represent interannual isotope variability accurately. However, common signal variance is diminished at lower (decadal and longer period) frequencies. This implies a need for increased sample replication in order to achieve chronology confidence equivalent to that routinely produced for simple ring width data. This work demonstrates that significant high-frequency climate signals are contained in isotopic measurements of trees whose ring widths contain little or no such information.
Physical and Inflammatory Stressors Elevate Circadian Clock Gene mPer1 mRNA Levels in the Paraventricular Nucleus of the Mouse.

Stress induces secretion of corticosterone through activation of the hypothalamic-pituitary-adrenal axis. This corticosterone secretion is thought to be controlled by a circadian clock in the suprachiasmatic nucleus (SCN). The hypothalamic paraventricular nucleus (PVN) receives convergent information from both stress and the circadian clock. Recent reports demonstrate that mammalian orthologs (Per1, Per2, and Per3) of the Drosophila clock gene Period are expressed in the SCN, PVN, and peripheral tissues. In this experiment, we examined the effect of physical and inflammatory stressors on mPer gene expression in the SCN, PVN, and liver. Forced swimming, immobilization, and lipopolysaccharide injection elevated mPer1 gene expression in the PVN but not in the SCN or liver. A stress-induced increase in mPer1 expression was observed in the corticotropin-releasing factor-positive cells of the PVN; however, the stressors used in this study did not affect mPer2 expression in the PVN, SCN, or liver. The present study suggests that a stress-induced disturbance of circadian corticosterone secretion may be associated with the stress-induced expression of mPer1 mRNA in the PVN.
Modelling faecal coliform concentrations in streams

This report examines the mechanisms of faecal and is successfully applied to routine monitoring coliforn transport and die-off on the land and in data for the River Exe in Devon. Climate change the aquatic environment. Equations derived from scenarios are examined for the driest and wettest these investigations are used to develop a predictions forthe year 2050: these result ina 5.6% mathematicalmodel of faecal coliform dynamics reduction and a 1. 6% increase in faecal coliform in streams and rivers. Process equations concentrations, respectively. Aregionalmodel, describingthe keydie-offmechanisms inthe using GIS techniques to relate faecal coliform aquatic environment are derived frompublished concentration to land-use, shows a strong data. A novel approach is used to describe the correlationbetween agriculturalland-use and entrainment of organisms which have settled to faecal coliform concentration. The regionalmodel the river bed: this is based on field observations could be used to describe diffuse inputs to the duringflow releases from reservoirs. Adead-zone river model. Applications forthis work include approach is used to model mixing and dispersion water quality planning to examine the effects of mechanisms, as well as simple flow routing land-use change, changes in sewage effluent equations and terms specific to faecal coliform discharges, water supply protection, estimation of dynamics, including settlement and entrainment, faecal coliform loads to the coastal zone, and and die-off due to sunlight, temperature and pH. assessment of health risks associatedwith The model accurately reproduces the field data recreational use offreshwaters.
Anestesia en procedimientos lumboscópicos: Experiencia en el Centro Nacional de Cirugía de mínimo acceso

I Especialista de I Grado en Anestesiologia y Reanimacion. Msc Urgencias Medicas Instructor. Investigadora Agregada. Centro Nacional de Cirugia de Minimo Acceso. Ciudad Habana. II Especialista de II Grado en Urologia. Investigadora Auxiliar. Profesora Auxiliar. Centro Nacional de Cirugia de Minimo Acceso. Ciudad Habana. III Especialista de I Grado en Anestesiologia y Reanimacion. Investigador Agregado. Profesor Auxiliar. Centro Nacional de Cirugia de Minimo Acceso. Ciudad Habana. IV Especialista de I Grado en Anestesiologia y Reanimacion. Instructor. Centro Nacional de Cirugia de Minimo Acceso. Ciudad Habana.
Rab Proteins and the Compartmentalization of the Endosomal System

Endosomal System Rab Proteins and the Compartmentalization of the Angela Wandinger-Ness and Marino Zerial Clathrin-Mediated Endocytosis Endocytic Accessory Factors and Regulation of Christien J. Merrifield and Marko Kaksonen Regulator of Cell Polarity and Tissue Dynamics Cargo Sorting in the Endocytic Pathway: A Key Suzanne Eaton and Fernando Martin-Belmonte System The Complex Ultrastructure of the Endolysosomal Judith Klumperman and Graça Raposo
Two adjacent forested catchments: Dramatically different NO3− export

Two adjacent catchments with similar temperate forest cover and podzolic soils have annual nitrate (NO3−) export that differs by a factor of 10. Monthly rates of mineralization and nitrification measured by the buried bag technique, soil C/N ratios, and the contribution of microbial NO3− to total NO3− in the groundwater as determined by analysis of δ18O in NO3− are also similar. In both catchments, maximum NO3− export occurs during spring melt, but in the catchment with higher export, NO3− concentrations in the stream begin to increase in the fall period. Groundwater NO3− concentrations measured in wells are very different in the two catchments with high groundwater NO3− in the catchment exhibiting high NO3− export. Following spring melt, steeper slopes in the high NO3− catchment promote faster drainage, and the water table declines rapidly while high NO3− concentrations are maintained in groundwaters. Deeper water tables will preserve high NO3− in water infiltrating below the rooting zone and organic‐rich upper soil horizons. In the low NO3− catchment, slower drainage on shallower slopes lead to an increase in soil saturation, and the NO3− disappears from the water before the water table declines. Analyses of δ15N in NO3− during NO3− loss do not show evidence of denitrification, although denitrification proceeding to completion in isolated pockets followed by mixing with higher NO3− groundwaters would yield the same result. Alternatively, active uptake of NO3− by vegetation following spring melt will also deplete the groundwater NO3− in the shallow soil depths without isotopic fractionation. The low NO3− catchment also has lower NO3− in shallow soil waters during spring melt. Shallower slopes promote near‐surface flow paths in organic‐rich soil horizons which may facilitate denitrification during spring melt. Although the catchment with low NO3− export has a large wetland near the catchment outlet, the NO3− attenuating capacity of this wetland is largely unused except in the late fall because growing season groundwater concentrations of NO3− are undetectable and the wetland is frozen during snowmelt. In the high NO3− catchment, organic‐rich soils and vegetation in the riparian zone cannot completely attenuate high NO3− in discharging groundwaters. In our study, factors controlling NO3− in groundwater such as slope, stratigraphy, and hydraulic conductivity can play a larger role than riparian zones in controlling differences in annual NO3− export observed between catchments.
Inference of transcriptional regulatory network by two-stage constrained space factor analysis

MOTIVATION Microarray gene expression and cross-linking chromatin immunoprecipitation data contain voluminous information that can help the identification of transcriptional regulatory networks at the full genome scale. Such high-throughput data are noisy however. In contrast, from the biomedical literature, we can find many evidenced transcription factor (TF)-target gene binding relationships that have been elucidated at the molecular level. But such sporadically generated knowledge only offers glimpses on limited patches of the network. How to incorporate this valuable knowledge resource to build more reliable network models remains a question. RESULTS We present a modified factor analysis approach. Our algorithm starts with the evidenced TF-gene linkages. It iterates between the network configuration estimation step and the connection strength estimation step, using the high-throughput data, till convergence. We report two comprehensive regulatory networks obtained for Saccharomyces cerevisiae, one under the normal growth condition and the other under the environmental stress condition. SUPPLEMENTARY INFORMATION http://kiefer.stat.ucla.edu/lap2/download/bti656_supplement. pdf.
Event-related causality in Stereo-EEG discriminates syntactic processing of noun phrases and verb phrases

Syntax involves complex neurobiological mechanisms, which are difficult to disentangle for multiple reasons. Using a protocol able to separate syntactic information from sound information we investigated the neural causal connections evoked by the processing of homophonous phrases, either verb phrases (VP) or noun phrases (NP). We used event-related causality (ERC) from stereo-electroencephalographic (SEEG) recordings in 10 epileptic patients in multiple cortical areas, including language areas and their homologous in the non-dominant hemisphere. We identified the different networks involved in the processing of these syntactic operations (faster in the dominant hemisphere) showing that VPs engage a wider cortical network. We also present a proof-of-concept for the decoding of the syntactic category of a perceived phrase based on causality measures. Our findings help unravel the neural correlates of syntactic elaboration and show how a decoding based on multiple cortical areas could contribute to the development of speech prostheses for speech impairment mitigation.
CALL FOR PAPERS Biomarkers in Lung Diseases: from Pathogenesis to Prediction to New Therapies Endothelin-1 induces VCAM-1 expression-mediated inflammation via receptor tyrosine kinases and Elk/p300 in human tracheal smooth muscle cells

Lin CC, Lin WN, Hou WC, Hsiao LD, Yang CM. Endothelin-1 induces VCAM-1 expression-mediated inflammation via receptor tyrosine kinases and Elk/p300 in human tracheal smooth muscle cells. Am J Physiol Lung Cell Mol Physiol 309: L211–L225, 2015. First published June 12, 2015; doi:10.1152/ajplung.00232. 2014. —The elevated level of endothelin-1 (ET-1) has been detected in the bronchoalveolar lavage of patients with severe asthma, acute lung injury, acute respiratory distress syndrome, and sepsis. ET-1 may affect vessel tone together with lung physiology and pathology. Vascular cell adhesion molecule-1 (VCAM-1) is one kind of adhesion molecules participating in the process of polymorphonuclear leukocyte transmigration and regulating the occurrence and amplification of tissue inflammation. However, the molecular mechanisms underlying ET-1-mediated expression of VCAM-1 on human tracheal smooth muscle cells (HTSMCs) were largely unknown. Here we reported that ET-1 stimulated expression of VCAM-1 gene on HTSMCs, which was blocked by pretreatment with the inhibitors of ET receptors, Src, matrix metalloproteinases (MMPs), epidermal growth factor receptor (EGFR), platelet-derived growth factor receptor (PDGFR), phosphatidylinositol 3-kinase (PI3K), AKT, MEK1/2, and p300, suggesting the participation of these signaling components in ET-1-regulated HTSMC responses. Furthermore, transfection with small-interfering RNA (siRNA) of Src, AKT, p42 mitogen-activated protein kinase (MAPK), or p300 downregulated the respective proteins and significantly attenuated ET-1-induced VCAM-1 expression. ET-1 also stimulated phosphorylation of Src, EGFR, PDGFR, AKT, p42/p44 MAPK, and Elk-1 and acetylation of histone H4 on HTSMCs. Immunoprecipitation assay showed the association between Elk-1 and p300 in the nucleus. Adhesion assay revealed that the adhesion of THP-1 to HTSMCs challenged with ET-1 was increased, which was attenuated by the inhibitors of ET receptors, Src, MMPs, EGFR, PDGFR, PI3K, AKT, p42/p44 MAPK, and p300. Taken together, these data suggested that ET-1 promotes occurrence and amplification of pathology-related airway inflammation via enhancing VCAM-1 expression in an ET receptor/Src/MMP/EGFR, PDGFR/PI3K/AKT/ p42/p44 MAPK/Elk-1/p300 pathway in HTSMCs.