Miracle-dz/UniFAR-FTUs huggingface dataset:
Capsules for Biomedical Image Segmentation

Our work expands the use of capsule networks to the task of object segmentation for the first time in the literature. This is made possible via the introduction of locally-constrained routing and transformation matrix sharing, which reduces the parameter/memory burden and allows for the segmentation of objects at large resolutions. To compensate for the loss of global information in constraining the routing, we propose the concept of "deconvolutional" capsules to create a deep encoder-decoder style network, called SegCaps. We extend the masked reconstruction regularization to the task of segmentation and perform thorough ablation experiments on each component of our method. The proposed convolutional-deconvolutional capsule network, SegCaps, shows state-of-the-art results while using a fraction of the parameters of popular segmentation networks. To validate our proposed method, we perform the largest-scale study in pathological lung segmentation in the literature, where we conduct experiments across five extremely challenging datasets, containing both clinical and pre-clinical subjects, and nearly 2000 computed-tomography scans. Our newly developed segmentation platform outperforms other methods across all datasets while utilizing 95% fewer parameters than the popular U-Net for biomedical image segmentation. We also provide proof-of-concept results on thin, tree-like structures in retinal imagery as well as demonstrate capsules' handling of rotations/reflections on natural images.
Structure of periplasmic trehalase from Diamondback moth gut bacteria in the apo form

Energy metabolism in the diamondback moth Plutella xylostella is facilitated by trehalase, an enzyme which assists in trehalose hydrolysis, from the predominant gut bacterium Enterobacter cloacae. We report the biochemical and structural characterization of recombinant trehalase from E. cloacae (Px_EclTre). Px_EclTre showed KM of 1.47 (±0.05) mm, kcat of 6254.72 min-1 and Vmax 0.2 (±0.002) mm·min-1 at 55 °C and acidic pH. Crystal structures of Px_EclTre were determined in the ligand-free form and bound to the inhibitor Validoxylamine A. The crystal structure of the ligand-free form, unavailable until now for any other bacterial trehalases, enabled us to delineate the conformational changes accompanying ligand binding in trehalases. Multiple salt bridges were identified that potentially facilitated closure of a hood over the substrate-binding site. A cluster of five tryptophans lined the -1 substrate-binding subsite, interacted with crucial active site residues and contributed to both trehalase activity and stability. The importance of these residues in enzyme activity was further validated by mutagenesis studies. Many of these identified residues form part of signature motifs and other conserved sequences in trehalases. The structure analysis thus led to the assignment of the functional role to these conserved residues. This information can be further explored for the design of effective inhibitors against trehalases.
An evaluation of deep convective mixing in the Goddard Chemical Transport Model using International Satellite Cloud Climatology Project cloud parameters

The simulation of deep convective mixing in the Goddard Chemical Transport Model (GCTM) is evaluated by comparing 1990-1992 distributions of upper tropospheric convective mass flux and cloud top pressure from the Goddard Earth Observing System data assimilation system (GEOS-1 DAS) with deep convective cloud fields from the International Satellite Cloud Climatology Project (ISCCP). Deep convective mixing in the GCTM is calculated using convective information from the GEOS-1 DAS. Therefore errors introduced when deep convection is parameterized in the GEOS-1 DAS affect the distribution of trace gases in the GCTM. The location of deep convective mixing in the tropics is fairly well simulated, although its north-south extent is overestimated by >5°. The frequency of deep convective mixing also appears to be overestimated in the tropics, resulting in GCTM-calculated upper tropospheric concentrations of carbon monoxide in the tropics that are larger and less variable than those observed. The spatial extent of deep convective mixing in the subtropics is overestimated at several locations including the Caribbean throughout the year and the South Pacific Convergence Zone during June-August. The extent of deep convection is underestimated over midlatitude marine storm tracks. DAS-calculated cloud top pressures differ from ISCCP cloud top pressures by less than one-half a GCTM layer (35 hPa) at most longitudes in the tropics; however, cloud top pressures are overestimated by more than 35 hPa (i.e., the vertical extent of deep convection is underestimated) over wintertime midlatitude storm tracks and the Indian Ocean and underestimated by more than 35 hPa at locations that include the Gulf of Mexico during December-February and central South America during June-August.
Asymmetry in the current sheet and secondary magnetic flux ropes during guide field magnetic reconnection

A magnetic reconnection event with a moderate guide field encountered by Cluster in the near-Earth tail on 28 August 2002 is reported. The guide field points dawnward during this event. The quadrupolar structure of the Hall magnetic field within the ion diffusion region is distorted toward the northern hemisphere in the earthward part while toward the southern hemisphere tailward part of X-line. Observations of current density and electron pitch angle distribution indicate that the distorted quadrupolar structure is formed due to a deformed Hall electron current system. Cluster crossed the ion diffusion region from south to north earthward of the X-line. An electron density cavity is confirmed in the northern separatrix layer while a thin current layer (TCL) is measured in the southern separatrix layer. The TCL is formed due to electrons injected into the X-line along the magnetic field. These observations are different from simulation results where the cavity is produced associated with inflow electrons along the southern separatrix while the strong current sheet appears with the outflow electron beam along the northern separatrix. The energy of the inflowing electron in the separatrix layer could extend up to 10 keV. Energetic electron fluxes up to 50 keV have a clear peak in the TCL. The length of the separatrix layer is estimated to be at least 65 c/omega(pi). These observations suggest that electrons could be pre-accelerated before they are ejected into the X-line region along the separatrix. Multiple secondary flux ropes moving earthward are observed within the diffusion region. These secondary flux ropes are all identified earthward of the observed TCL. These observations further suggest there are numerous small scale structures within the ion diffusion region.
Responses to a Warming World

Animal and plant life cycles are increasingly shown to depend on temperature trends and patterns. In their Perspective, PeA±uelas and Filella review the evidence that global warming during the 20th century has affected the growth period of plants and the development and behavior of animals from insects to birds. The authors warn that changes in the interdependence between species could have unpredictable consequences for ecosystems, that the lengthening of the plant growing season contributes to the global increased carbon fixation, and that changes in phenology may affect not only ecosystems but also agriculture and sanitation.
Sound velocities in MgSiO3‐garnet to 8 GPa

Velocities of acoustic compressional (P) and shear (S) waves were measured to 8 GPa at room temperature for dense (99.7% of theoretical density), isotropic polycrystalline specimens of MgSiO3‐majorite garnet using the phase comparison method of ultrasonic interferometry in a 1000‐ton split‐cylinder apparatus (USCA‐1000). The pressure derivatives of the adiabatic bulk modulus (KS) and the shear modulus (G) are Ko′ = (∂Ks/∂P)T =6.7±0.4 and Go′ = (∂G/∂P)T =1.9±0.1. Substitution of Si for Mg and Al in these garnets increase Ko′ by 26%, and Go′ by 16%, from Mg3Al2Si3O12‐pyrope to majorite. The high values of Ko′ and Go′ from this study lead to much steeper velocity‐depth profiles in the transition zone (400–700 km) than those calculated from the Ko′ and Go′ estimates from elasticity systematics by Duffy and Anderson (1989).
Social preferences for fuel break management programs in Spain: a choice modelling application to prevention of forest fires

This article reports on an economic valuation study of alternative fire prevention programs in the province of Malaga, southern Spain. The main aim of this study was to explore the social preferences for several forest fire prevention management issues. Fuel break programs were presented that differed in terms of cleaning technique (controlled grazing, prescribed burning and mechanical treatments), design (from traditional linear unshaded fire breaks to more landscape and environmentally friendly structures, such as shaded fuel breaks) and density (linked to annual burnt area). RESULTS show that the population was clearly interested in the potential of the proposed programs to reduce fire. Lessons learnt from this study could be relevant for the development of fire prevention policies and specific prevention campaigns in Mediterranean forests.
Traumatic Imagery following Glucocorticoid Administration in Earthquake-Related PTSD: A Preliminary fMRI Study

Objective: Post-traumatic stress disorder (PTSD) involves excessive retrieval of traumatic memories. Glucocorticoids impair declarative memory retrieval. This preliminary study examined the effect of acute hydrocortisone administration on brain activation in individuals with earthquake-related PTSD compared with earthquake-exposed healthy individuals, during retrieval of traumatic memories. Method: Participants exposed to earthquakes with ( n =11) and without PTSD ( n =11) underwent two fMRI scans, one-week apart, in a double-blind, placebo-controlled, counter-balanced design. On one occasion they received oral hydrocortisone (20mg), and on the other, placebo, one hour before scanning. Symptom provocation involved script-driven imagery (traumatic and neutral scripts) and measures of self-reported anxiety. Results: Arterial spin labelling showed that both PTSD and trauma-exposed controls had significantly reduced cerebral blood flow in response to retrieval of traumatic versus neutral memories in the right hippocampus, parahippocampal gyrus, calcarine sulcus, middle and superior temporal gyrus, posterior cingulate, heschls gyrus, inferior parietal lobule, angular gyrus, middle occipital gyrus, supramarginal gyrus, lingual gyrus and cuneus, and the left prefrontal cortex. Hydrocortisone resulted in non-significant trends of increasing subjective distress and reduced regional cerebral blood flow in the left inferior frontal gyrus, left anterior cingulate gyrus, middle temporal gyrus, cerebellum, post central gyrus and right frontal pole, during the trauma script. Conclusion: Findings do not fit with some aspects of the accepted neurocircuitry model of PTSD, i.e., failure of the medial prefrontal cortex to quieten hyperresponsive amygdala activity, and the potential therapeutic benefits of hydrocortisone. They do, however, provide further evidence that exposure to earthquake trauma, regardless of whether PTSD eventuates, impacts on brain activity and highlights the importance of inclusion of trauma-exposed comparisons in studies of PTSD.
Pregnancy outcomes in mixed connective tissue disease: a multicentre study

University of Turin’s Institutional Research Information System and Open Access Institutional Repository This is the author's final version of the contribution published as: Rheumatology (Oxford). 2019 Nov 1;58(11):2000-2008. doi: 10.1093/rheumatology/kez141. Pregnancy outcomes in mixed connective tissue disease: a multicentre study. Radin M, Schreiber K, Cuadrado MJ, Cecchi I, Andreoli L, Franceschini F, Caleiro T, Andrade D, Gibbone E, Khamashta M, Buyon J, Izmirly P, Aguirre MA, Benedetto C, Roccatello D, Marozio L, Sciascia S. PMID: 31079145
Pregnancy outcomes in mixed connective tissue disease: a multicentre study

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Intracellular trafficking , localization , and mobilization of platelet borne thiol

Crescente, M. , Pluthero, F. G. , Li, L. , Lo, R. W. , Walsh, T. G. , Schenk, M. P., Holbrook, L. M. , Loureiro, S. , Ali, M. S. , Vaiyapuri, S. , Falet, H. , Jones, I. M. , Poole, A. W. , Kahr, W. H. A. and Gibbins, J. M. (2016) Intracellular trafficking, localization, and mobilization of platelet­borne thiol isomerases. Arteriosclerosis Thrombosis and Vascular Biology, 36 (6). pp. 1164­1173. ISSN 1079­5642 doi: https://doi.org/10.1161/ATVBAHA.116. 307461 Available at http://centaur.reading. ac.uk/64077/
A simple quantitative model of plasma flows and currents in Saturn's polar ionosphere

[1] We propose a simple illustrative axisymmetric model of the plasma flows and currents that occur in Saturn's polar ionosphere which are due to both internal magnetospheric plasma processes and the solar wind interaction. The features of the model are based on previous physical discussion, guided quantitatively by both Voyager plasma observations on closed field lines and remote-sensing IR Doppler observations on open field lines. With increasing latitude the flow features represented include a region poleward of ∼25° colatitude where the angular velocities decrease continuously from rigid corotation to ∼60% of rigid corotation due to plasma production from internal sources in the central magnetosphere, a narrow band of higher but still subcorotating angular velocities mapping to Dungey cycle return flow and Vasyliunas cycle flow regions in the outer closed field magnetosphere, and, finally, a region of low angular velocities, ∼30% of rigid corotation, on open field lines in the polar cap. We show that these flows require a four-region pattern of field-aligned currents. With increasing latitude, these consist of regions of upward and downward current on closed field lines peaking at a few tens of nanoamperes per square meter (for an effective ionospheric Pedersen conductivity of 1 mho), a narrow ring of upward field-aligned current across the open-closed field line boundary of order 100 nA m−2, and distributed downward currents on open field lines of order 10 nA m−2. Of the upward currents, only that at the open-closed field line boundary is of sufficient intensity to require significant acceleration of magnetospheric electrons, resulting in total precipitating electron powers of ∼0.03–0.06 TW, together with auroral UV emissions of a few tens of kilorayleighs. The latter emissions occur in a ring of a few hundred kilometers latitudinal width at ∼13° colatitude, which we thus associate with Saturn's main auroral oval. We also estimate similar powers in unaccelerated electron precipitation on closed field lines equatorward of the boundary, leading to distributed “diffuse” UV emissions of a fraction of a kilorayleigh. However, by far the most important energy input to the polar upper atmosphere is due to Joule heating by the ionospheric Pedersen currents, which we estimate as typically several milliwatts per square meter poleward of ∼20° colatitude. The overall Joule powers are estimated to be ∼2.5 TW on both open and closed field lines in each hemisphere (for a conductivity of ∼1 mho and no slippage of the neutral atmosphere), thus representing a very significant energy input to Saturn's thermosphere, more than an order of magnitude larger than the globally averaged solar input. Joule heating is thus likely to make a significant contribution to an explanation of why Saturn's thermosphere is observed to be hot, ∼400–600 K, compared with less than ∼200 K expected on the basis of solar heating alone.
Nup358 interacts with APC and plays a role in cell polarization

Asymmetric localization of adenomatous polyposis coli (APC) to the ends of a subset of microtubules located in the leading edges is essential for the establishment of front-rear polarity during cell migration. APC is known to associate with microtubules in three ways: through interaction with the plus-end tracking protein EB1, direct binding through a C-terminal basic region, and through interaction with the plus-end motor kinesin-2. Here we report that the middle region of APC has a previously unidentified microtubule plus-end-targeting function, suggesting an additional microtubule-binding mode for APC. Through the same region, APC interacts with Nup358 (also called RanBP2), a microtubule-binding nucleoporin. Ectopic expression of the middle region of APC is sufficient to recruit endogenous Nup358 to the plus ends of microtubules. Furthermore, our results indicate that Nup358 cooperates with kinesin-2 to regulate the localization of APC to the cell cortex through a nuclear-transport-independent mechanism. Using RNA interference and a scratch-induced wound-healing assay we demonstrate that Nup358 functions in polarized cell migration. These results reveal a more active role for structural nucleoporins in regulating fundamental cellular processes than previously anticipated.
Arabidopsis HD-Zip II transcription factors control apical embryo development and meristem function

The Arabidopsis genome encodes ten Homeodomain-Leucine zipper (HD-Zip) II proteins. ARABIDOPSIS THALIANA HOMEOBOX 2 (ATHB2), HOMEOBOX ARABIDOPSIS THALIANA 1 (HAT1), HAT2, HAT3 and ATHB4 are regulated by changes in the red/far red light ratio that induce shade avoidance in most of the angiosperms. Here, we show that progressive loss of HAT3, ATHB4 and ATHB2 activity causes developmental defects from embryogenesis onwards in white light. Cotyledon development and number are altered in hat3 athb4 embryos, and these defects correlate with changes in auxin distribution and response. athb2 gain-of-function mutation and ATHB2 expression driven by its promoter in hat3 athb4 result in significant attenuation of phenotypes, thus demonstrating that ATHB2 is functionally redundant to HAT3 and ATHB4. In analogy to loss-of-function mutations in HD-Zip III genes, loss of HAT3 and ATHB4 results in organ polarity defects, whereas triple hat3 athb4 athb2 mutants develop one or two radialized cotyledons and lack an active shoot apical meristem (SAM). Consistent with overlapping expression pattern of HD-Zip II and HD-Zip III gene family members, bilateral symmetry and SAM defects are enhanced when hat3 athb4 is combined with mutations in PHABULOSA (PHB), PHAVOLUTA (PHV) or REVOLUTA (REV). Finally, we show that ATHB2 is part of a complex regulatory circuit directly involving both HD-Zip II and HD-Zip III proteins. Taken together, our study provides evidence that a genetic system consisting of HD-Zip II and HD-Zip III genes cooperates in establishing bilateral symmetry and patterning along the adaxial-abaxial axis in the embryo as well as in controlling SAM activity.
“New” lunar meteorites: Impact melt and regolith breccias and large‐scale heterogeneities of the upper lunar crust

Abstract— We have analyzed nine highland lunar meteorites (lunaites) using mainly INAA. Several of these rocks are difficult to classify. Dhofar 081 is basically a fragmental breccia, but much of its groundmass features a glassy‐fluidized texture that is indicative of localized shock melting. Also, much of the matrix glass is swirly‐brown, suggesting a possible regolith derivation. We interpret Dar al Gani (DaG) 400 as an extremely immature regolith breccia consisting mainly of impact‐melt breccia clasts; we interpret Dhofar 026 as an unusually complex anorthositic impact‐melt breccia with scattered ovoid globules that formed as clasts of mafic, subophitic impact melt. The presence of mafic crystalline globules in a lunar material, even one so clearly impact‐heated, suggests that it may have originated as a regolith. Our new data and a synthesis of literature data suggest a contrast in Al2O3‐incompatible element systematics between impact melts from the central nearside highlands, where Apollo sampling occurred, and those from the general highland surface of the Moon. Impact melts from the general highland surface tend to have systematically lower incompatible element concentration at any given Al2O3 concentration than those from Apollo 16. In the case of Dhofar 026, both the bulk rock and a comparatively Al‐poor composition (14 wt% Al2O3, 7 μg/g Sm) extrapolated for the globules, manifest incompatible element contents well below the Apollo 16 trend. Impact melts from Luna 20 (57°E) distribute more along the general highland trend than along the Apollo 16 trend. Siderophile elements also show a distinctive composition for Apollo 16 impact melts: Ni/Ir averaging ˜1.8x chondritic. In contrast, lunaite impact‐melt breccias have consistently chondritic Ni/Ir. Impact melts from Luna 20 and other Apollo sites show average Ni/Ir almost as high as those from Apollo 16. The prevalence of this distinctive Ni/Ir ratio at such widely separated nearside sites suggests that debris from one extraordinarily large impact may dominate the megaregolith siderophile component of a nearside region 2300 km or more across.
DEM Analysis of Stresses and Deformations of Geogrid-Reinforced Embankments over Piles

AbstractThe geosynthetic-reinforced pile-supported embankment is one of the favorable ground improvement techniques used in the construction of earth structures over a compressible soil when limited construction time is available and limited deformation is permissible. Various methods are available for the design of the geosynthetic-reinforced platform based on various load transfer mechanisms from the embankment to the piles and the compressible soil. The existence of the geosynthetic layer makes the mechanisms more complex. This study focuses on the behavior of geogrid-reinforced embankments over piles compared with the behavior of unreinforced embankments. The numerical simulations of the unreinforced and reinforced pile-supported embankments were conducted using the discrete element method (DEM). The embankment fill was simulated using unbonded graded aggregates of diameters ranging from 9.2 to 20.8 mm and the geogrid was simulated using bonded particles. This study investigated the changes of vertica.