Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate Automated Segmentation of Autophagic Bodies in Yeast Vacuoles Using Cellpose 2.0

Segmenting autophagic bodies in yeast TEM images is a key technique for measuring changes in autophagosome size and number in order to better understand autophagy. Manual segmentation of these images can be very time consuming, particularly since hundreds of images are needed for accurate measurements. Here we describe a validated Cellpose 2.0 model that can segment these images with accuracy comparable to that of human experts. This model can be used for fully automated segmentation, eliminating the need for manual body outlining, or for model-assisted segmentation, which allows human oversight but is still five times as fast as the current manual method. The model and instructions for its use are presented here for the autophagy community.
Microglia contribute to methamphetamine reinforcement and reflect persistent transcriptional and morphological adaptations to the drug

Methamphetamine use disorder (MUD) is a chronic, relapsing disease that is characterized by repeated drug use despite negative consequences and for which there are currently no FDA-approved cessation therapeutics. Repeated methamphetamine (METH) use induces long-term gene expression changes in brain regions associated with reward processing and drug-seeking behavior, and recent evidence suggests that methamphetamine-induced neuroinflammation may also shape behavioral and molecular responses to the drug. Microglia, the resident immune cells in the brain, are principal drivers of neuroinflammatory responses and contribute to the pathophysiology of substance use disorders. Here, we investigated transcriptional and morphological changes in dorsal striatal microglia in response to methamphetamine-taking and during methamphetamine abstinence, as well as their functional contribution to drug-taking behavior. We show that methamphetamine self-administration induces transcriptional changes associated with protein folding, mRNA processing, immune signaling, and neurotransmission in dorsal striatal microglia. Importantly, many of these transcriptional changes persist through abstinence, a finding supported by morphological analyses. Functionally, we report that microglial ablation increases methamphetamine-taking, possibly involving neuroimmune and neurotransmitter regulation, and that post-methamphetamine microglial repopulation attenuates drug-seeking following a 21-day period of abstinence. In contrast, microglial depletion during abstinence did not alter methamphetamine-seeking. Taken together, these results suggest that methamphetamine induces both short and long-term changes in dorsal striatal microglia that contribute to altered drug-taking behavior and may provide valuable insights into the pathophysiology of MUD. GRAPHICAL ABSTRACT
Classical to Relaxor Ferroelectric Transformation of Lanthanum Modified BaTi0.91Sn0.09O3 Ceramics

Abstract Lead-free Ba1-xLaxTi0.91Sn0. 09O3 (BLTS) ceramics with x = 0, 0.01, 0.03 and 0.05, were prepared by the traditional solid-state sintering method with calcination and sintering temperatures of 1200 °C for 2 h and 1400 °C for 4 h, respectively. X-ray diffraction (XRD) measurements revealed that all the BLTS ceramics had pure perovskite structures with no detectable impurities. When x = 0 and 0.01, the ceramics exhibited coexisting orthorhombic (O) and tetragonal (T) phases, while the orthorhombic (O), tetragonal (T) and cubic phase (C) were detected in the BLTS ceramics with x = 0.03 and 0.05, which the Rietveld refinement analysis confirmed. Furthermore, increasing x in the BLTS ceramics led to a large decrease in the average grain size (from 45.7 to 0.9 µm). A significant decrease in the remnant polarization (P r) accompanied by very slim hysteresis loops were observed for higher La (x ≥ 0.03) levels. This demonstrates that BLTS ceramics transition from classical ferroelectric to relaxor ferroelectric behavior due to changing occupancy of the A-site to La3+ from Ba2+.
Regulator of G protein signaling 6 (RGS6) in ventral tegmental area (VTA) dopamine neurons promotes EtOH seeking, behavioral reward and susceptibility to relapse

Mesolimbic dopamine (DA) transmission is believed to play a critical role in mediating reward responses to drugs of abuse, including alcohol (EtOH). EtOH is the most abused substance worldwide with chronic consumption often leading to the development of dependence and abuse. Unfortunately, the neurobiological mechanisms underlying EtOH-seeking behavior and dependence are not fully understood, and abstinence remains the only effective way to prevent alcohol use disorders (AUDs). Here, we developed novel RGS6fl/fl; DAT-iCreER mice to determine the role of RGS6 in VTA DA neurons on EtOH consumption and reward behaviors. We found that RGS6 is expressed in DA neurons in both human and mouse VTA, and that RGS6 loss in mice upregulates DA transporter (DAT) expression in VTA DA neuron synaptic terminals. Remarkably, loss of RGS6 in VTA DA neurons significantly reduced EtOH consumption, preference, and reward in a manner indistinguishable from that seen in RGS6−/− mice. Strikingly, RGS6 loss from VTA DA neurons before or after EtOH behavioral reward is established significantly reduced (∼50%) re-instatement of reward following extinguishment, demonstrating distinct roles of RGS6 in promoting reward and relapse susceptibility to EtOH. These studies illuminate a critical role of RGS6 in the mesolimbic circuit in promoting EtOH seeking, reward, and reinstatement. We propose that RGS6 functions to promote DA transmission through its function as a negative modulator of GPCR-Gαi/o-DAT signaling in VTA DA neurons. These studies identify RGS6 as a potential therapeutic target for behavioral reward and relapse to EtOH.
Joint location and source mechanism inversion of microseismic events: benchmarking on seismicity induced by hydraulic fracturing

SUMMARY Seismic monitoring can greatly benefit from imaging events with a low signal-to-noise ratio (SNR) as the number of the events with a low signal grows exponentially. One way to detect weaker events is improvement of a SNR by migration-type stacking of waveforms from multiple stations. We have developed a new method of location of seismic events that involves stackingofseismicphasesandamplitudesalongdiffractiontraveltimecurvestosuppressnoise and detect seismic events with a SNR lower than that on individual receivers. The stacking includes polarity correction based on a simultaneous seismic moment tensor inversion and detection algorithm on the stack function. We applied this method to locate microseismicity induced by hydraulic fracturing. First we calibrated the velocity model by locating perforation shots at known locations. Then we processed 3 d of data from microseismic monitoring of shale stimulation and benchmarked migration-type locations of the largest events that were manually located. The detected and located events induced by hydraulic fracturing in this case study are mostly shear events forming narrow bands along the maximum horizontal stress direction approximately 100 m above the injection intervals. The proposed technique is fully automated and feasible for real-time seismic monitoring.
Use of fault striations and dislocation models to infer tectonic shear stress during the 1995 Hyogo-Ken Nanbu (Kobe) earthquake

Dislocation models of the 1995 Hyogo-ken Nanbu (Kobe) earthquake derived by Yoshida et al. (1996) show substantial changes in direction of slip with time at specific points on the Nojima and Rokko fault systems, as do striations we observed on exposures of the Nojima fault surface on Awaji Island. Spudich (1992) showed that the initial stress, that is, the shear traction on the fault before the earthquake origin time, can be derived at points on the fault where the slip rake rotates with time if slip velocity and stress change are known at these points. From Yoshida's slip model, we calculated dynamic stress changes on the ruptured fault surfaces. To estimate errors, we compared the slip velocities and dynamic stress changes of several published models of the earthquake. The differences between these models had an exponential distribution, not gaussian. We developed a Bayesian method to estimate the probability density function (PDF) of initial stress from the striations and from Yoshida's slip model. Striations near Toshima and Hirabayashi give initial stresses of about 13 and 7 MPa, respectively. We obtained initial stresses of about 7 to 17 MPa at depths of 2 to 10 km on a subset of points on the Nojima and Rokko fault systems. Our initial stresses and coseismic stress changes agree well with postearthquake stresses measured by hydrofracturing in deep boreholes near Hirabayashi and Ogura on Awaji Island. Our results indicate that the Nojima fault slipped at very low shear stress, and fractional stress drop was complete near the surface and about 32% below depths of 2 km. Our results at depth depend on the accuracy of the rake rotations in Yoshida's model, which are probably correct on the Nojima fault but debatable on the Rokko fault. Our results imply that curved or cross-cutting fault striations can be formed in a single earthquake, contradicting a common assumption of structural geology.
Analytical determination of limit-cycle pollutant concentrations in small tidal embayments

This paper describes the development of a novel mathematical model for predicting the water quality response of small tidal harbours and marinas which are subjected to a continuous release of conservative pollutant. The model is based upon a 'tidal prism' or 'zero-dimensional' approach and uses a simple analytical technique to predict the periodic variations in pollutant concentration. The mathematical model provides a viable and computationally inexpensive alternative to conventional multi-dimensional pollution transport simulations and offers an insight into the interrelationship between the main physical parameters which govern the dispersion of pollution from a tidal harbour.Predictions from the analytical formulation are compared with experimental pollution data from a 1:400 scale laboratory model of a generic square harbour. The results indicate that the tidal prism approach offers a simple yet robust method of determining the water quality response of well-mixed tidal basins.
Abstract: Microbially induced sedimentary structures in the Carboniferous Horton Bluff Formation near Hantsport, Nova Scotia

The Hurd Creek Member of the Horton Bluff Formation comprises cyclic tidal deposits of early Mississippian age. Near Hantsport, microbially induced sedimentary structures, formed by the growth of cyanobacterial mats, are unusually well preserved on the bedding surfaces of quartz-rich siltstones. The structures match those documented from modern sediments at Mellum Island, North Sea and Archean strata at Barberton, South Africa. The sediments display wrinkle structures and leveled depositional surfaces, in association with wave ripples, planed-off ripples, and desiccation cracks that imply shallow-water and periodically exposed conditions. A single, well exposed surface was mapped in one-metre segments with estimates of the areal percentage of microbial features, descriptions of the main types present, and photographs. The outcrop is ~70 m long and 1 m wide, selected for its high quality and quantity of microbial features. Microbial structures cover 12.6% of the exposed surface. Wrinkles are sub-parallel or lack preferred orientation, and have 1 mm height and 1-2 mm spacing – much smaller than associated ripple marks. The wrinkled patches often occur on ripple crests, especially on flattened, planedoff areas, and are commonly associated with coarse, probably windblown, sand. Some wrinkled patches cover sediment that fills ripple troughs, where mat growth has contributed to levelling of the sediment surface. Desiccation cracks are present, implying that these quartz-rich strata were unusually cohesive, perhaps due to microbial binding. Similar microbial features are present on many other bedding surfaces, and microbial effects were pervasive during deposition. Microbial effects indicated by wrinkle structures, leveled depositional surfaces and desiccation cracks are complemented by observations from hand specimens and thin sections that suggest an unusual degree of cohesion shortly after deposition. Dark, 1 mm thick wavy-crinkly laminae drape over mounds of sand in ways that are not characteristic of physical deposition. Large, 0.5 mm quartz grains are embedded in these dark laminae and may reflect the microbial process of sediment-grain separation. Individual quartz grains rest in unusual positions, probably bound by dark laminae. Broken fragments of dark laminae are folded and display frayed edges.
Dior-CVAE: Diffusion Priors in Variational Dialog Generation

Conditional variational autoencoders (CVAEs) have been used recently for diverse response generation, by introducing latent variables to represent the relationship between a dialog context and its potential responses. However, the diversity of the generated responses brought by a CVAE model is limited due to the over-simplified assumption of the isotropic Gaussian prior. We propose, Dior-CVAE, a hierarchical CVAE model with an informative prior produced by a diffusion model. Dior-CVAE derives a series of layer-wise latent variables using attention mechanism and infusing them into decoder layers accordingly. We propose memory dropout in the latent infusion to alleviate posterior collapse. The prior distribution of the latent variables is parameterized by a diffusion model to introduce a multimodal distribution. Overall, experiments on two popular open-domain dialog datasets indicate the advantages of our approach over previous Transformer-based variational dialog models in dialog response generation. We publicly release the code for reproducing Dior-CVAE and all base-lines at https://github.com/SkyFishMoon/ Latent-Diffusion-Response-Generation .
Fine Phenotyping of Pod and Seed Traits in Arachis Germplasm Accessions Using Digital Image Analysis

ABSTRACT Reliable and objective phenotyping of peanut pod and seed traits is important for cultivar selection and genetic mapping of grade components. To develop useful and efficient methods to quantitatively define peanut pod and seed traits, a group of peanut germplasm with high levels of phenotypic variation was included in this study. Digital image analysis was employed to quantify peanut pod volume using projected 2-dimensional pod area as an effective surrogate parameter. Strong correlation between pod volume measured by water displacement and image analysis was established (R2 = 0.891). Pod volume, pod density and kernel percent were observed to vary significantly among the germplasm lines. To define testa color, hue angle analysis was performed on a subset of germplasm with solid testa color. It was determined that hue angle can sufficiently differentiate genotypic differences based on testa color variation.
Combined Use of Groundwater Dating, Chemical, and Isotopic Analyses to Resolve the History and Fate of Nitrate Contamination in Two Agricultural Watersheds, Atlantic Coastal Plain, Maryland

The history and fate of groundwater nitrate (NO3−) contamination were compared in 2 small adjacent agricultural watersheds in the Atlantic coastal plain by combined use of chronologic (CCl2F2, 3H), chemical (dissolved solids, gases), and isotopic (δ15N,δ13C, δ34S) analyses of recharging groundwaters, discharging groundwaters, and surface waters. The results demonstrate the interactive effects of changing agricultural practices, groundwater residence times, and local geologic features on the transfer of NO3− through local flow systems. Recharge dates of groundwaters taken in 1990–1992 from the surficial aquifer in the Chesterville Branch and Morgan Creek watersheds near Locust Grove, Maryland, ranged from pre-1940 to the late 1980’s. When corrected for localized denitrification by use of dissolved gas concentrations, the dated waters provide a 40-year record of the recharge rate of NO3−, which increased in both watersheds by a factor of 3–6, most rapidly in the 1970's. The increase in groundwater NO3− over time was approximately proportional to the documented increase in regional N fertilizer use, and could be accounted for by oxidation and leaching of about 20–35% of the fertilizer N. Groundwaters discharging upward beneath streams in both watersheds had measured recharge dates from pre-1940 to 1975, while chemical data for second-order reaches of the streams indicated average groundwater residence times in the order of 20+ years. At the time of the study, NO3− discharge rates were less than NO3− recharge rates for at least two reasons: (1) discharge of relatively old waters with low initial NO3− concentrations, and (2) local denitrification. In the Chesterville Branch watershed, groundwaters remained oxic throughout much of the surficial aquifer and discharged relatively unaltered to the stream, which had a relatively high NO3− concentration (9–10 mg/L as N). In the Morgan Creek watershed, groundwaters were largely reduced and denitrified before discharging to the stream, which had a relatively low NO3− concentration (2–3 mg/L as N). Chemical and isotopic data indicate that quantitative denitrification occurred within buried calcareous glauconitic marine sediments that are present at relatively shallow depths beneath the Morgan Creek watershed. NO3− removal by forests, wetlands, and shallow organic-rich soils in near-stream environments was largely avoided by groundwaters that followed relatively deep flow paths before converging and discharging rapidly upward to the streams.
Impact of utilities distribution in the population scattering: one analyzes of the African reality -Huambo Angola

The migratory phenomenon has been familiar with different realities, where less expectable regions can win or lose its population density influenced by factors whose compression can help to rethinking the forms of urban structure. The numerous studies on population trends and migratory flow the densification of urban centers and related to aspects such as social security, land productivity, life quality, employment and accessibility to socials services that can cause changes in the way population is scattered by territory. This reality is evident in developing countries who face mobility of its labor force in search of better opportunities in the more urbanized locations, leaving marks on economic or in regions that lose population, as well as those who earn. Therefore, realizing the real impact of employment in population distribution, in order to understand the impact that particular activity exercises can be an economic development strategy and ensuring the welfare for many countries in sub-Saharan Africa where 60 percents of the urban population are ? in Slum conditions'. And, Angola is in this reality not only for its geographical context, but, by the existence of numerous factors that systematically attract the population from rural to per-urban areas, increasing the population density of urban centers at the same rate that degrades the life quality. Surprisingly this evidence, few studies have devoted attention to understand the dynamics of population flow and its implications. Around this problematic the problem is: what policies or governance measures can redirect the current urban densification? Has a certain economic factors and urban restructuring impact in the population sprinkling? Or, will the jobs associated with basic services such as education and health, influence in the population grouping to the point of creating new intermediate centers? Or own population density is that it tends to attract these jobs? Considering to these questions, the study aims to estimate the impact of the allocation of public services (education and health) in population distribution, and seeks to understand the interaction between public services and spatial distribution of population. Using a spatial interaction model developed in MatLab, we formulate up five study scenarios of jobs distribution and analyzed data through, of Angola National Development Plan 2013 -2017,. The results are not only a management tool in the urbanization process that is required in locations rapidly growing, as in the case of Huambo city. That as the country's environment of fruit watching a rural exodus that could collapse the sustainability of existing urban scepters, more like also the results are very suggestive to understand the causes of migration and the constraints to the development of centralities.
GENERALIZATION OF RAYLEIGH MAXIMUM LIKELIHOOD DESPECKLING FILTER USING QUADRILATERAL KERNELS

Speckle noise is the most prevalent noise in clinical ultrasound images. It visibly looks like light and dark spots and deduce the pixel intensity as murkiest. Gazing at fetal ultrasound images, the impact of edge and local fine details are more palpable for obstetricians and gynecologists to carry out prenatal diagnosis of congenital heart disease. A robust despeckling filter has to be contrived to proficiently suppress speckle noise and simultaneously preserve the features. The proposed filter is the generalization of Rayleigh maximum likelihood filter by the exploitation of statistical tools as tuning parameters and use different shapes of quadrilateral kernels to estimate the noise free pixel from neighborhood. The performance of various filters namely Median, Kuwahura, Frost, Homogenous mask filter and Rayleigh maximum likelihood filter are compared with the proposed filter in terms PSNR and image profile. Comparatively the proposed filters surpass the conventional filters.
2013). Pharmacokinetics of Modified-Release Prednisone Tablets in Healthy Subjects and Patients With Rheumatoid Arthritis. Journal of Clinical Pharmacology, 53(3), 326-33

In rheumatoid arthritis (RA), nocturnal release of pro-inflammatory cytokines is not adequately counteracted by endogenous glucocorticoid, and is associated with symptoms of morning stiffness and pain. Taking exogenous glucocorticoid during the night reduces morning stiffness significantly more than treatment at the conventional time in the morning, though waking to take tablets is unacceptable for patients. Modified-release prednisone tablets have beenwas developed to allow administration at bedtime for programmed delivery of glucocorticoid during the night. Single centre crossover studies were conducted, each in ≥24 healthy subjects, to compare the pharmacokinetics of a single 5 mg oral dose of modified-release prednisone and conventional prednisone, and the effect of food on bioavailability. There was no substantial difference in pharmacokinetic parameters of the formulations apart from the programmed delay in release of glucocorticoid from the modified-release tablets (C max 97%, AUC 0-∞ 101%, 90% confidence intervals within the requisite range for bioequivalence). Administration after a full or light meal did not affect pharmacokinetic characteristics, but bioavailability was reduced under fasted conditions. Pharmacokinetic evaluation in nine patients with RA confirmed that modified-release prednisone tablets taken at bedtime (around 22:00 h) with or after an evening meal result in programmed release of glucocorticoid 4–6 hours after intake.