Miracle-dz/UniFAR-FTUs huggingface dataset:
Menin regulates the serine biosynthetic pathway in Ewing sarcoma

Developmental transcription programs are epigenetically regulated by multi‐protein complexes, including the menin‐ and MLL‐containing trithorax (TrxG) complexes, which promote gene transcription by depositing the H3K4me3 activating mark at target gene promoters. We recently reported that in Ewing sarcoma, MLL1 (lysine methyltransferase 2A, KMT2A) and menin are overexpressed and function as oncogenes. Small molecule inhibition of the menin–MLL interaction leads to loss of menin and MLL1 protein expression, and to inhibition of growth and tumorigenicity. Here, we have investigated the mechanistic basis of menin–MLL‐mediated oncogenic activity in Ewing sarcoma. Bromouridine sequencing (Bru‐seq) was performed to identify changes in nascent gene transcription in Ewing sarcoma cells, following exposure to the menin–MLL interaction inhibitor MI‐503. Menin–MLL inhibition resulted in early and widespread reprogramming of metabolic processes. In particular, the serine biosynthetic pathway (SSP) was the pathway most significantly affected by MI‐503 treatment. Baseline expression of SSP genes and proteins (PHGDH, PSAT1, and PSPH), and metabolic flux through the SSP were confirmed to be high in Ewing sarcoma. In addition, inhibition of PHGDH resulted in reduced cell proliferation, viability, and tumor growth in vivo, revealing a key dependency of Ewing sarcoma on the SSP. Loss of function studies validated a mechanistic link between menin and the SSP. Specifically, inhibition of menin resulted in diminished expression of SSP genes, reduced H3K4me3 enrichment at the PHGDH promoter, and complete abrogation of de novo serine and glycine biosynthesis, as demonstrated by metabolic tracing studies with 13C‐labeled glucose. These data demonstrate that the SSP is highly active in Ewing sarcoma and that its oncogenic activation is maintained, at least in part, by menin‐dependent epigenetic mechanisms involving trithorax complexes. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Nanoparticles, Nanocrystals, and Nanocomposites Produced with Pulsed Laser Ablation and Their Applications

In the last few decades, nanoparticles have become key components in a variety of appli- cations in nanotechnology, nanoengineering, and nanoscience. Pulsed laser ablation in liquids (PLAL) method is frequently preferred for fast and pure nanoparticle generation. There exists a wide range of metal and semi-conductor nanoparticles that are successfully synthesized by PLAL method. In our research, nanoparticle synthesis of different materials and their applications are pursued. After nanoparticle synthesis, the application research proceeds and the scope of the research spans many subjects ranging from sensor realization to biological applications.
Creative professional users’ musical relevance criteria

Although known item searching for music can be dealt with by searching metadata using existing text search techniques, human subjectivity and variability within the music itself make it very difficult to search for unknown items. This paper examines these problems within the context of text retrieval and music information retrieval. The focus is on ascertaining a relationship between music relevance criteria and those relating to relevance judgements in text retrieval. A data-rich collection of relevance judgements by creative professionals searching for unknown musical items to accompany moving images using real world queries is analysed. The participants in our observations are found to take a socio-cognitive approach and use a range of content- and context-based criteria. These criteria correlate strongly with those arising from previous text retrieval studies despite the many differences between music and text in their actual content.
meta-PPISP: a meta web server for protein-protein interaction site prediction

UNLABELLED A number of complementary methods have been developed for predicting protein-protein interaction sites. We sought to increase prediction robustness and accuracy by combining results from different predictors, and report here a meta web server, meta-PPISP, that is built on three individual web servers: cons-PPISP (http://pipe.scs.fsu.edu/ppisp.html), Promate (http://bioportal.weizmann.ac.il/promate), and PINUP (http://sparks.informatics.iupui.edu/PINUP/). A linear regression method, using the raw scores of the three servers as input, was trained on a set of 35 nonhomologous proteins. Cross validation showed that meta-PPISP outperforms all the three individual servers. At coverages identical to those of the individual methods, the accuracy of meta-PPISP is higher by 4.8 to 18.2 percentage points. Similar improvements in accuracy are also seen on CAPRI and other targets. AVAILABILITY meta-PPISP can be accessed at http://pipe.scs. fsu.edu/meta-ppisp.html
Shot, Scene and Keyframe Ordering for Interactive Video Re-use

This paper presents a complete system for shot and scene detection in broadcast videos, as well as a method to select the best representative key-frames, which could be used in new interactive interfaces for accessing large collections of edited videos. The final goal is to enable an improved access to video footage and the re-use of video content with the direct management of user-selected video-clips.
DE-BONDING STRANDS AS AN ANCHORAGE ZONE CRACK CONTROL METHOD FOR PRETENSIONED CONCRETE BULB-TEE BRIDGE GIRDERS USING NONLINEAR FINITE ELEMENT ANALYSIS

Cracks occurring in the anchorage zones of pre-tensioned bridge girders after de-tensioning are a concern because of the possibility of de-icing salts corroding steel reinforcing bars or strands within concrete. This study assessed the efficacy of strand debonding for crack control by instrumenting and simulating full-scale bridge girders with varying ratios of debonded strands (25%, 38% and 62%). Strand debonding over a distance larger than the transfer length and over a short distance from the girder end was investigated. Although 25% debonding reduced strains, it was not sufficient to eliminate cracks. De-bonding 38% of the strands at the girder ends eliminated cracks causing corrosion concerns. Debonding 62% of strands for a short distance resulted in similar or smaller strains in concrete compared to a girder with no debonding.
Hierarchical congestion control for robotic swarms

Safe and efficient navigation of robotic swarms is an important research problem. One of the main challenges in this area is to avoid congestion, which usually happens when large groups of robots share the same environment. In this paper, we propose the use of hierarchical abstractions in conjunction with simple traffic control rules based on virtual forces to avoid congestion in swarm navigation. We perform simulated and real experiments in order to study the feasibility and effectiveness of the proposed algorithm. Results show that our approach allows the swarm to navigate without congestions in a smooth and coherent fashion, being suitable for large groups of robots.
Optimal construction of subband coders using Lloyd-Max quantizers

A new method is presented for the analysis of the effects of Lloyd-Max quantization in subband filterbanks and for the optimal design of such filterbanks. A rigorous statistical model of a vector Lloyd-Max quantizer is established first, consisting of a linear time-invariant filter followed by additive noise uncorrelated/with the input. On the basis of this model, an expression for this variance of the error of a subband coder using Lloyd-Max quantizers is explicitly determined. Given analysis filters that statistically separate the subbands, it is shown that this variance is minimized if the synthesis filters are chosen, which mould achieve perfect reconstruction in lossless coding. The globally optimum of such a filterbank, minimizing the coder error variance, is further obtained by proper choice of its analysis filters. An alternative design method is also evaluated and optimized. In this, the errors correlated with the signal are set to zero, leaving a random error residue uncorrelated with the signal. This design method is optimized by choosing the analysis filters so as to minimize the random error variance. The results are evaluated experimentally in the realistic setting of a logarithmically split subband image coding scheme.
Application of the random coupling model to lossy ports in complex enclosures

The random coupling model (RCM) has been successfully demonstrated to characterize the statistics of the impedance matrix for complex multi-port cavities. However, a challenge remains in finding a practical method to measure the necessary parameters that form the model, especially in the case where ports have localized power loss. In this paper, we present practical methods to measure the radiation impedance of the port and the loss parameter of the cavity. In the case of lossy port in the complex cavity, a generalized antenna model is adopted, and the radiation efficiency of the antenna is used to modify RCM's impedance description.
Elites are people, too: The effects of threat sensitivity on policymakers’ spending priorities

Recent research suggests that psychological needs can influence the political attitudes of ordinary citizens, often outside of their conscious awareness. In this paper, we investigate whether psychological needs also shape the spending priorities of political elites in the US. Most models of policymaking assume that political elites respond to information in relatively homogeneous ways. We suggest otherwise, and explore one source of difference in information processing, namely, threat sensitivity, which previous research links to increased support for conservative policy attitudes. Drawing on a sample of state-level policymakers, we measure their spending priorities using a survey and their level of threat sensitivity using a standard psychophysiological measure (skin conductance). We find that, like ordinary citizens, threat sensitivity leads even state-level policymakers to prioritize spending on government polices that are designed to minimize threats.
Necrotizing Soft Tissue Infection: Diagnostic Accuracy of Physical Examination, Imaging, and LRINEC Score A Systematic Review and Meta-Analysis

Objective: We sought to summarize accuracy of physical examination, imaging, and Laboratory Risk Indicator for Necrotizing Fasciitis (LRINEC) score in diagnosis of necrotizing soft tissue infection (NSTI) in adults with a soft tissue infection clinically concerning for NSTI. Summary of Background Data: NSTI is a life-threatening diagnosis. Delay to diagnosis and surgical management is associated with increased mortality. Methods: We searched 6 databases from inception through November 2017. We included English-language studies reporting diagnostic accuracy of testing or LRINEC Score. Outcome was NSTI confirmed by surgery or histopathology. Two reviewers screened all citations and extracted data independently. Summary measures were obtained from the Hierarchical Summary Receiver Operating Characteristic model. Results: From 2,290 citations, we included 23 studies (n = 5982). Of physical examination signs, pooled sensitivity and specificity for fever was 46.0% and 77.0% respectively, for hemorrhagic bullae 25.2% and 95.8%, and for hypotension 21.0% and 97.7%. Computed tomography (CT) had sensitivity of 88.5% and specificity of 93.3%, while plain radiography had sensitivity of 48.9% and specificity of 94.0%. Finally, LRINEC ≥ 6 had sensitivity of 68.2% and specificity of 84.8%, while LRINEC ≥ 8 had sensitivity of 40.8% and specificity of 94.9%. Conclusions: Absence of any 1 physical examination feature (eg, fever or hypotension) is not sufficient to rule-out NSTI. CT is superior to plain radiography. LRINEC had poor sensitivity, and should not be used to rule-out NSTI. Given the poor sensitivity of these tests, a high clinical suspicion warrants early surgical consultation for definitive diagnosis and management.
Chemoresistance to Cancer Treatment: Benzo-α-Pyrene as Friend or Foe?

Background: Environmental pollution such as exposure to pro-carcinogens including benzo-α-pyrene is becoming a major problem globally. Moreover, the effects of benzo-α-pyrene (BaP) on drug pharmacokinetics, pharmacodynamics, and drug resistance warrant further investigation, especially in cancer outpatient chemotherapy where exposure to environmental pollutants might occur. Method: We report here on the effects of benzo-α-pyrene on esophageal cancer cells in vitro, alone, or in combination with chemotherapeutic drugs cisplatin, 5-flurouracil, or paclitaxel. As the study endpoints, we employed expression of proteins involved in cell proliferation, drug metabolism, apoptosis, cell cycle analysis, colony formation, migration, and signaling cascades in the WHCO1 esophageal cancer cell line after 24 h of treatment. Results: Benzo-α-pyrene had no significant effect on WHCO1 cancer cell proliferation but reversed the effect of chemotherapeutic drugs by reducing drug-induced cell death and apoptosis by 30–40% compared to drug-treated cells. The three drugs significantly reduced WHCO1 cell migration by 40–50% compared to control and BaP-treated cells. Combined exposure to drugs was associated with significantly increased apoptosis and reduced colony formation. Evaluation of survival signaling cascades showed that although the MEK-ERK and Akt pathways were activated in the presence of drugs, BaP was a stronger activator of the MEK-ERK and Akt pathways than the drugs. Conclusion: The present study suggest that BaP can reverse the effects of drugs on cancer cells via the activation of survival signaling pathways and upregulation of anti-apoptotic proteins such as Bcl-2 and Bcl-xL. Our data show that BaP contribute to the development of chemoresistant cancer cells.
Resonant Raman spectroscopy of nanotubes

Single and double resonances in Raman scattering are introduced and six criteria for the observation and identification of double resonances stated. The experimental situation in carbon nanotubes is reviewed in view of these criteria. The evidence for the D mode and the high–energy mode is found to be overwhelming for a double–resonance process to take place, whereas the nature of the radial breathing–mode Raman process remains undecided at this point. Consequences for the application of Raman scattering to the characterization of nanotubes are discussed.
Estimating Evapotranspiration by Remote Sensing and Water Management Applications

Ground-based, air-borne, and space-borne remote sensing techniques have evolved over the past several decades and provided many new techniques for estimating various land surface attributes at multiple scales related to mass and energy dynamics. The vadose zone, encompassing land surface, root zone, and the deeper soil profile down to the groundwater table, is a complex domain, particularly related to various hydrologic and biological processes across different scales. In this zone, spatial distributions and temporal dynamics of soil moisture and evapotranspiration (ET), including their interdependence, are critical to climate feedback, hydrology, and plant canopy health. Their temporal and spatial variability across catchments affect surface and subsurface runoff, modulates evaporation and transpiration, determines the extent of groundwater recharge and contaminant transport, and initiates or sustains feedback between the land surface and the atmosphere. With the recent development and deployment of various remote sensing platforms working with different techniques such as optical, microwave, gravitational, infrared, and other sensors, improved temporal and spatial measurement or estimates of soil moisture, evapotranspiration, soil hydraulic parameters, soil salinity, and vegetation attributes are possible. In this special section “Remote Sensing for Vadose Zone Hydrology,” 14 contributions on fundamental and applied studies using different remote sensing platforms, including satellite retrieval algorithm development, data assimilation techniques, scaling issues, ground validation, and field applications in the context of vadose zone hydrology are presented. The foci of these papers range across root zone soil moisture retrieval and variability, evapotranspiration dynamics and distribution, agricultural water management, soil hydraulic and mechanical property estimation, ecosystems assessment, land–atmosphere interaction, and land surface hazard assessment. Here we organized the summary of these papers in four overlapping sections including (i) estimation, variability, scaling, and data assimilation of soil moisture by microwave remote sensing; (ii) estimating evapotranspiration by remote sensing and water management applications; (iii) estimating vadose zone properties by remote sensing; and (iv) ground-based soil moisture for calibration and validation of microwave remote sensing.
Mixed Logical Inference and Probabilistic Planning for Robots in Unreliable Worlds

Deployment of robots in practical domains poses key knowledge representation and reasoning challenges. Robots need to represent and reason with incomplete domain knowledge, acquiring and using sensor inputs based on need and availability. This paper presents an architecture that exploits the complementary strengths of declarative programming and probabilistic graphical models as a step toward addressing these challenges. Answer Set Prolog (ASP), a declarative language, is used to represent, and perform inference with, incomplete domain knowledge, including default information that holds in all but a few exceptional situations. A hierarchy of partially observable Markov decision processes (POMDPs) probabilistically models the uncertainty in sensor input processing and navigation. Nonmonotonic logical inference in ASP is used to generate a multinomial prior for probabilistic state estimation with the hierarchy of POMDPs. It is also used with historical data to construct a beta (meta) density model of priors for metareasoning and early termination of trials when appropriate. Robots equipped with this architecture automatically tailor sensor input processing and navigation to tasks at hand, revising existing knowledge using information extracted from sensor inputs. The architecture is empirically evaluated in simulation and on a mobile robot visually localizing objects in indoor domains.
Sleep characteristics of family caregivers of individuals with a primary malignant brain tumor.

PURPOSE/OBJECTIVES To describe the sleep characteristics of family caregivers of individuals with a primary malignant brain tumor (PMBT). DESIGN Cross-sectional, correlational design using baseline data from a longitudinal study. SETTING Neuro-oncology and neurosurgery clinics at an urban tertiary medical center in the United States. SAMPLE 133 family caregivers recruited one to two months following diagnosis of family member's PMBT. METHODS Subjective and objective measures of sleep were obtained via self-report and the use of accelerometers (three nights). MAIN RESEARCH VARIABLES Sleep characteristics including sleep latency, total sleep time, wake after sleep onset, number of naps, number of arousals, sleep-wake cycle, and sleep quality. FINDINGS Sleep latency in caregivers was, on average, 35 minutes (SD = 34.5)-more than twice as long as the norm of 15 minutes (t[113]) = 6.18, p < 0.01). Caregivers averaged a total sleep time of 5 hours and 57 minutes (SD = 84.6), significantly less than the recommended 7 hours (t[113] = -8, p < 0.01), and were awake in the night 15% of the time, significantly more than the norm of 10% (t[111] = 5.84, p < 0.01). Caregivers aroused an average of 8.3 times during nocturnal sleep (SD = 3.5, range = 2-21), with about 32% reporting poor or very poor sleep quality. CONCLUSIONS Caregivers experienced sleep impairments that placed them at risk for poor mental and physical health, and may compromise their ability to continue in the caregiving role. IMPLICATIONS FOR NURSING Nurses need to assess sleep in caregivers of individuals with PMBT and implement interventions to improve sleep. KNOWLEDGE TRANSLATION Sleep deprivation is common in family caregivers during the early stages of care for individuals with a PMBT. A single-item sleep quality question could be an easy but valuable tool in assessing sleep disturbances in family caregivers of individuals with a PMBT. The health trajectory of family caregivers warrants further longitudinal study, in addition to the examination of the bidirectional relationship of health status of care recipients and their family caregiver.
Assessment of Uncertainty in Geological Sites Based on Data Clustering and Conditional Probabilities

Geological investigations are carried out under particularly high uncertainties. Assessment of these uncertainties is very important for project planning. This paper presents a methodology to evaluate uncertainty associated with geological structures such as ore deposits and aquifers. In order to assess the uncertainty of the geological systems observed, fuzzy clustering and spatial measures are used. Then, the heterogeneous zones are evaluated using conditional probabilities. The posterior probabilities obtained from testing data provide useful information for assessing the uncertainty. © 2007 World Academic Press, UK. All rights reserved.
A Review of Annulation

AnnulationS, derived from the Latin work annulatus (ringed) means “the formation of rings”. ’ In organic chemistry this term is used to describe the process of building a ring onto a preexisting system. cyclic or non-cyclic. The added ring may be of any size, although 5and ~membered rings are most commonly formed. This broad de~nition includes in a general sense many reactions that are not normally thought of as annulation reactions, such as Diels-Alder reactions. ’ acid-catalyzed polyolefinic cyclizations,’ photochemical,’ radical,‘ and thermal’ cyclizations. This discussion will be concerned mainly with those processes of annulation which involve construction of a cyclohexenone ring onto a me-existing ketone; e.g. 1 -+t. These processes normally involve the
Modelling of heating of plasma-chemical reactor in Comsol Multiphysics.

For the thermophysical calculation of the reactor, a mathematical model was developed in Comsol Multiphysics, describing physical processes in the plasma-chemical reactor at a stationary mode. To simplify the calculation at this stage, it was carried out for an air plasma torch. The model includes two processes: fluid dynamic and heat transfer ones. As a result of the mathematical modelling the following parameters were obtained: temperature distribution in the reactor at steady state, average mass temperature in the reaction volume, velocity field and others.
BACE 1 transcription through NF-κ B and accelerates A β production and memory de fi cit in Alzheimer ’ s disease mouse model

Accumulation of amyloid β protein (Aβ)-containing neuritic plaques in the brain is a neuropathological feature of Alzheimer's disease (AD). The β-site APP-cleaving enzyme 1 (BACE1) is essential for Aβ generation and dysregulation of BACE1 expression may lead to AD pathogenesis. Bcl-2-associated athanogen 1M (BAG-1M), initially identified as an anti-apoptotic protein, has also been found to be highly expressed in the same neurons that contain intracellular amyloid in the hippocampus of AD patient. In this report, we found that overexpression of BAG-1M enhances BACE1-mediated cleavage of amyloid precursor protein (APP) and Aβ production by up-regulating BACE1 gene transcription. The regulation of BACE1 transcription by BAG-1M was dependent on NF-κB, as BAG-1M complexes NF-κB at the promoter of BACE1 gene and co-activates NF-κBfacilitated BACE1 transcription. Moreover, expression of BAG-1M by lentiviral vector in the hippocampus of AD transgenic model mice promotes Aβ generation and formation of neuritic plaque, and subsequently accelerates memory deficits of the mice. These results provide evidence for an emerging role of BAG-1M in the regulation of BACE1 expression and AD pathogenesis and that targeting the BAG-1M-NF-κB complex may provide a mechanism for inhibiting Aβ production and plaque formation.