Miracle-dz/UniFAR-FTUs huggingface dataset:
SART1 localizes to spindle poles forming a SART1 cap and promotes spindle pole assembly

The nuclear protein SART1 has been associated with pre-mRNA splicing but SART1 RNAi knockdown results also in defects in mitotic progression, centrosome biogenesis and chromosome cohesion. The mitotic roles of SART1 have not been characterized in detail and it remains unclear whether SART1 functions in mitosis directly or indirectly via pre-mRNA splicing. Here, we identify SART1 as a direct, mitosis-specific microtubule-associated protein. SART1 downregulation in human cells leads to spindle assembly defects with reduced microtubule dynamics, lack of end-on attachment, and checkpoint activation, while microtubule dynamics remain unaffected in interphase. SART1 uniquely localizes to the distal surface of mitotic centrosomes along the spindle axis, forming a previously not described structure we refer to as SART1 cap. Immunoprecipitation of SART1 consistently identifies centrosomal proteins as interaction partners. Immunostaining of these shows that SART1 downregulation does not affect centriole duplication and centrosome-accumulation of γ-tubulin but reduces the accumulation of selective pericentriolar material (PCM) proteins like Ninein. Depletion of SART1 from frog egg extracts disrupts spindle pole assembly around sperm nuclei and DNA-coated beads. Spindles formed around DNA-coated beads do not contain centrosomes but still recruits PCM proteins for spindle pole assembly. We finally show that the N-terminus of SART1 is its microtubule-binding region and essential for spindle assembly. Our data unravel a unique localization of SART1 and a novel function to recruit selective PCM proteins for spindle pole assembly in centrosomal and acentrosomal spindle assembly.
Assessing mechanical agency during apical apoptotic cell extrusion

Epithelial tissues maintain homeostasis through the continual addition and removal of cells. Homeostasis is necessary for epithelia to maintain barrier function and prevent the accumulation of defective cells. Unfit, excess, and dying cells can be removed from epithelia by the process of extrusion. Controlled cell death and extrusion in the epithelium of the larval zebrafish tail fin coincides with oscillation of cell area, both in the extruding cell and its neighbors. Both cell-autonomous and non-autonomous factors have been proposed to contribute to extrusion but have been challenging to test by experimental approaches. Here we develop a dynamic cell-based biophysical model that recapitulates the process of oscillatory cell extrusion to test and compare the relative contributions of these factors. Our model incorporates the mechanical properties of individual epithelial cells in a two-dimensional simulation as repelling active particles. The area of cells destined to extrude oscillates with varying durations or amplitudes, decreasing their mechanical contribution to the epithelium and surrendering their space to surrounding cells. Quantitative variations in cell shape and size during extrusion are visualized by a hybrid weighted Voronoi tessellation technique that renders individual cell mechanical properties directly into an epithelial sheet. To explore the role of autonomous and non-autonomous mechanics, we vary the biophysical properties and behaviors of extruding cells and neighbors such as the period and amplitude of repulsive forces, cell density, and tissue viscosity. Our data suggest that cell autonomous processes are major contributors to the dynamics of extrusion, with the mechanical microenvironment providing a less pronounced contribution. Our computational model based on in vivo data serves as a tool to provide insights into the cellular dynamics and localized changes in mechanics that promote elimination of unwanted cells from epithelia during homeostatic tissue maintenance.
A Layered Microcircuit Model of Somatosensory Cortex with Three Interneuron Types and Cell-Type-Specific Short-Term Plasticity

Three major types of GABAergic interneurons, the parvalbumin-(PV), somatostatin-(SOM) and vasoactive intestinal peptide-expressing (VIP) cells, play critical but distinct roles in the cortical microcircuitry. Their inhibitory functions are shaped by their specific electrophysiology and connectivity. To study how this diversity contributes to the dynamics and signal processing in the cerebral cortex, we developed a multi-layer model incorporating biologically realistic parameters of these interneurons from rodent somatosensory cortex. With in vivo data as criteria, the model shows plausible resting-state activity and responses to sensory stimulation. With a protocol of cell-type-specific stimulation, network responses when activating different neuron types are examined. The model reproduces the experimentally observed inhibitory effects of PV and SOM cells and disinhibitory effect of VIP cells on excitatory cells. In addition, responses of VIP cells to cell-type-specific stimulation provide predictions for future experiments. We further create a version of the model incorporating cell-type-specific short-term synaptic plasticity (STP). While the ongoing activity with and without STP is similar, STP modulates the responses of SOM and VIP cells to cell-type-specific stimulation, presumably by changing the dominant inhibitory pathways. Our model can serve to explore the computational roles of inhibitory interneurons and short-term synaptic plasticity in sensory functions.
Exploring the feasibility of a nationwide earthquake early warning system in Italy

When accompanied by appropriate training and preparedness of a population, Earthquake Early Warning Systems (EEWS) are effective and viable tools for the real‐time reduction of societal exposure to seismic events in metropolitan areas. The Italian Accelerometric Network, RAN, which consists of about 500 stations installed over all the active seismic zones, as well as many cities and strategic infrastructures in Italy, has the potential to serve as a nationwide early warning system. In this work, we present a feasibility study for a nationwide EEWS in Italy obtained by the integration of the RAN and the software platform PRobabilistic and Evolutionary early warning SysTem (PRESTo). The performance of the RAN‐PRESTo EEWS is first assessed by testing it on real strong motion recordings of 40 of the largest earthquakes that have occurred during the last 10 years in Italy. Furthermore, we extend the analysis to regions that did not experience earthquakes by considering a nationwide grid of synthetic sources capable of generating Gutenberg‐Richter sequences corresponding to the one adopted by the seismic hazard map of the Italian territory. Our results indicate that the RAN‐PRESTo EEWS could theoretically provide for higher seismic hazard areas reliable alert messages within about 5 to 10 s and maximum lead times of about 25 s. In case of large events (M > 6.5), this amount of lead time would be sufficient for taking basic protective measures (e.g., duck and cover, move away from windows or equipment) in tens to hundreds of municipalities affected by large ground shaking.
How does forest structure affect root reinforcement and susceptibility to shallow landslides?

Forests can decrease the risk of shallow landslides by mechanically reinforcing the soil and positively influencing its water balance. However, little is known about the effect of different forest structures on slope stability. In the study area in St Antönien, Switzerland, we applied statistical prediction models and a physically‐based model for spatial distribution of root reinforcement in order to quantify the influence of forest structure on slope stability. We designed a generalized linear regression model and a random forest model including variables describing forest structure along with terrain parameters for a set of landslide and control points facing similar slope angle and tree coverage. The root distribution measured at regular distances from seven trees in the same study area was used to calibrate a root distribution model. The root reinforcement was calculated as a function of tree dimension and distance from tree with the root bundle model (RBMw). Based on the modelled values of root reinforcement, we introduced a proxy‐variable for root reinforcement of the nearest tree using a gamma distribution. The results of the statistical analysis show that variables related to forest structure significantly influence landslide susceptibility along with terrain parameters. Significant effects were found for gap length, the distance to the nearest trees and the proxy‐variable for root reinforcement of the nearest tree. Gaps longer than 20 m critically increased the susceptibility to landslides. Root reinforcement decreased with increasing distance from trees and is smaller in landslide plots compared to control plots. Furthermore, the influence of forest structure strongly depends on geomorphological and hydrological conditions. Our results enhance the quantitative knowledge about the influence of forest structure on root reinforcement and landslide susceptibility and support existing management recommendations for protection against gravitational natural hazards. Copyright © 2015 John Wiley & Sons, Ltd.
A to explore

experiments with various combinations of stressors demonstrate, in simpliﬁed landscape settings, the model’s potential: predicting colony dynamics and potential losses with and without varroa mites under different foraging conditions and under pesticide application. We also show how mitigation measures can be tested. 4. Synthesis and applications . BEEHAVE offers a valuable tool for researchers to design and focus ﬁeld experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will ﬁnd a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics.
Increased Signal in the Subarachnoid Space on Fluid-Attenuated Inversion Recovery Imaging Associated with the Clearance Dynamics of Gadolinium Chelate: A Potential Diagnostic Pitfall

BACKGROUND AND PURPOSE: Hyperintense CSF in the subarachnoid space (SAS) on fluid-attenuated inversion recovery (FLAIR) imaging has been reported in numerous pathologic conditions, including subarachnoid hemorrhage, meningitis, meningeal carcinomatosis, superior sagittal thrombosis, adjacent tumors, status epilepticus, and stroke. It has also been reported in otherwise healthy patients undergoing anesthesia with supplemental oxygen. We present a series of 11 patients with hyperintense CSF signal intensity in the SAS on FLAIR imaging after previous administration of gadolinium chelate. MATERIALS AND METHODS: Head MR images of patients who had a prior gadolinium-enhanced body, spine, or brain MR imaging and who had increased signal intensity in the SAS on FLAIR images were prospectively and retrospectively reviewed. Correlation was made with the clinical and laboratory findings. RESULTS: Eight of the 11 patients had negative findings on lumbar punctures. Seven patients had either chronic renal insufficiency or acute renal failure, but the remaining 4 had normal renal function. Nine patients had no other significant intracranial abnormalities, and 2 patients had acute infarcts remote from the CSF hyperintensity. One patient had follow-up studies at 24 and 48 hours, documenting resolution of the CSF hyperintensities. CONCLUSION: Given the sharp rise in volume of contrast-enhanced MR imaging studies, it is inevitable that some patients will have undergone a contrast-enhanced MR imaging 24–48 hours before an MR imaging of the brain. The neuroradiologist should be aware that previous administration of gadolinium chelate can cause increased signal intensity in the SAS on FLAIR imaging in patients with or without a history of renal insufficiency and without abnormalities known to disrupt the blood-brain barrier.
Context-Dependent Effects of Goal Primes

We provide evidence that goal priming effects are context dependent. We show that goal primes encourage prime-consistent behavior when the behavioral context is common and prime-inconsistent behavior when the behavioral context is uncommon. While the prime-consistent behavior is compatible with existing theory, the prime-inconsistent behavior poses a theoretical challenge. We argue that uncommon behavioral contexts encourage the release of a primed goal and, as a consequence, an increase in the relative activation of information inconsistent with the primed goal and prime-inconsistent behavior. (c) 2008 by JOURNAL OF CONSUMER RESEARCH, Inc.
Multi-session transcutaneous spinal cord stimulation prevents chloridehomeostasis imbalance and the development of spasticity after spinal cordinjury in rat

Spasticity is a complex and multidimensional disorder that impacts nearly 75% of individuals with spinal cord injury (SCI) and currently lacks adequate treatment options. This sensorimotor condition is burdensome as hyperexcitability of reflex pathways result in exacerbated reflex responses, co-contractions of antagonistic muscles, and involuntary movements. Transcutaneous spinal cord stimulation (tSCS) has become a popular tool in the human SCI research field. The likeliness for this intervention to be successful as a noninvasive anti-spastic therapy after SCI is suggested by a mild and transitory improvement in spastic symptoms following a single stimulation session, but it remains to be determined if repeated tSCS over the course of weeks can produce more profound effects. Despite its popularity, the neuroplasticity induced by tSCS also remains widely unexplored, particularly due to the lack of suitable animal models to investigate this intervention. Thus, the basis of this work was to use tSCS over multiple sessions (multi-session tSCS) in a rat model to target spasticity after SCI and identify the long-term physiological improvements and anatomical neuroplasticity occurring in the spinal cord. Here, we show that multi-session tSCS in rats with an incomplete (severe T9 contusion) SCI (1) decreases hyperreflexia, (2) increases the low frequency-dependent modulation of the H-reflex, (3) prevents potassium-chloride cotransporter isoform 2 (KCC2) membrane downregulation in lumbar motoneurons, and (4) generally augments motor output, i.e., EMG amplitude in response to single pulses of tSCS, particularly in extensor muscles. Together, this work displays that multi-session tSCS can target and diminish spasticity after SCI as an alternative to pharmacological interventions and begins to highlight the underlying neuroplasticity contributing to its success in improving functional recovery.
Pan-genome analysis of different morphotypes reveals genomic basis of Brassica oleracea domestication and differential organogenesis

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed with high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant (SV) hotspot regions enriched with auxin and flowering-related genes. Population genomic analyses reveal that early domestication of B. oleracea focused on leaf or stem selection. Gene flows resulting from agricultural practices and variety improvement are detected among different morphotypes. Selective sweep analysis identifies an auxin-responsive SAUR gene and a CLE family gene as the crucial players in the leaf-stem differentiation during the early stage of B. oleracea domestication, and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further discover that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.
Decoding spatial organization maps and context-specific landscapes of breast cancer and its microenvironment via high-resolution spatial transcriptomic analysis

Single-cell RNA transcriptomics has revealed the intricate heterogeneity of both tumors and their microenvironment. However, a notable limitation is its inability to retain spatial context, a crucial aspect of understanding cell identity and function. In this study, we employed imaging-based single-cell spatial transcriptomics to elucidate the tumor and immunological landscapes of two breast cancer samples. By resolving over 400 000 cells per slide, we demonstrated that transcriptional differences lead to structural disparities within and between tumors. Additionally, we observed that the composition of the tumor microenvironment varies depending on its spatial location. Notably, we detected immune cell gradients transitioning from the tumor periphery to its core regions and from tertiary lymphoid structure to immune inflamed regions, in alignment with the specific function of each cell type. This finding facilitated a more precise classification of the tumor immune microenvironment. This study provides a comprehensive dataset for breast cancer researchers and underscores the significance of spatial context in understanding the multifaceted heterogeneity of cancer and its environment.
QUANTITATIVE GEOMORPHOLOGICAL ANALYSIS FOR CHARACTERIZATION OF SELECTED WATERSHEDS IN WESTERN MAHARASHTRA

Morphometric analysis of a watershed provides a quantitative description of the drainage system, which is an important input for the characterization of watershed. Remote Sensing and Geographical Information System (RSGIS) techniques are in vogue for assessing various quantitative morphometric parameters of the drainage basins / watersheds, as they provide a user friendly environment and a powerful tool for the manipulation and analysis of spatial information. The shape, size and drainage pattern play a significant role in deciding the characterization of surface runoff and the locales favourable for groundwater recharge and discharge. On this background, three watersheds of different shapes and sizes were selected to undertake quantitative geomorphological analysis. Authors have evaluated the morphometric characteristics on the basis of Survey of India toposheets at 1:50,000 scale, and ASTER DEM data. The paper incorporates the comparison of drainage characteristics and their hydrogeological significance.
Europe and Global Imbalances

Although Europe in the aggregate is a not a major contributor to global current account imbalances, its trade and financial linkages with the rest of the world mean that it will still be affected by a shift in the current configuration of external deficits and surpluses. We assess the macroeconomic impact on Europe of global current account adjustment under alternative scenarios, emphasizing both trade and financial channels. Finally, we consider heterogeneous exposure across individual European economies to external adjustment shocks.
Downwardly Mobile The Accidental Cost of Being Uninsured

Results: Crude analysis revealed a higher mortality for uninsured patients (odds ratio [OR], 1.39; 95% confidence interval [CI], 1.36-1.42; P .001). Controlling for sex, race, age, Injury Severity Score, Revised Trauma Score, and injury mechanism (adjusted for clustering on hospital), uninsured patients had the highest mortality (OR, 1.80; 95% CI, 1.61-2.02; P .001). Subgroup analysis of young patients unlikely to have comorbidities revealed higher mortality for uninsured patients (OR, 1.89; 95% CI, 1.66-2.15; P .001), as did subgroup analyses of patients with head injuries (OR, 1.65; 95% CI, 1.42-1.90; P .001) and patients with 1 or more comorbidities (OR, 1.52; 95% CI, 1.30-1.78; P .001).
New Methods of Testing and Brain Imaging in Hepatic Encephalopathy

HE comprises a spectrum of neuropsychiatric manifestations that can occur in patients with cirrhosis, acute liver failure, acute-on-chronic liver failure, or major portosystemic shunting without intrinsic liver disease. It is characterized by disturbances in cognitive and motor function that can manifest as a change in personality, altered mood, diminished intellectual capacity, abnormal muscle tone, and tremor, among other symptoms in chronic liver disease. Themanifestations of this entity in acute liver failure can include abrupt-onset delirium, seizures, and coma as a result of cerebral
Cumulative Stress Burden and Cognitive Function in African American Adults Living in Low-Income Neighborhoods

African Americans (AA) are more likely to experience stressors due to racial discrimination and segregated neighborhoods, potentially contributing to higher risk for dementia. We investigated the association between stressors and cognitive function in older AA adults through cumulative stress burden (CSB) indices. Stressors and cognitive domains were measured in 253 participants >50 years, recruited from primarily AA neighborhoods in Pittsburgh, PA. CSB included perceived and psychological distress, unfair treatment, post-traumatic stress disorder, and neighborhood-level stressors such as walkability, safety, satisfaction, and social cohesion. Indices were formed by dichotomizing stressor scores and summing. Cognitive domains were z-scores adjusted for age, sex, and education. Adjusted generalized linear models assessed the relation between CSB indices and cognition, and between specific stressors and cognition. Interactions with age were tested. Greater individual-level CSB index was associated with lower language (□= -0.11, p= 0.03) and executive function (□= -0.087, p=0.04). The neighborhood-level CSB index was not associated with any cognitive domain. The combined index was marginally associated with language in adjusted models (□= -0.07, p= 0.05). There were no significant associations between specific stressors and cognition, except for neighborhood safety with 3MS (□= -0.28, p= 0.001) and language (□= -0.16, p= 0.02). Age interactions indicate that findings were stronger for younger participants. Greater cumulative stress is associated with poorer cognitive function in some domains in older AA. A comprehensive assessment of cumulative stress is vital in understanding the dimensionality of racialized stress for older adults potentially experiencing cognitive decline.