Miracle-dz/UniFAR-FTUs huggingface dataset:
STAT5 Gain-of-Function Variants Promote Precursor T-Cell Receptor Activation to Drive T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive immature T-cell cancer. Hotspot mutations in JAK-STAT pathway members IL7R, JAK1 and JAK3 were analyzed in depth. However, the role of STAT5A or STAT5B mutations promoting their hyperactivation is poorly understood in the context of T-cell cancer initiation and acute leukemia progression. Importantly, the driver mutation STAT5BN642H encodes the most frequent activating STAT5 variant in T-ALL associated with poor prognosis. Here, we show that hyperactive STAT5 promotes early T-cell progenitor (ETP)-ALL-like cancer in mice and upregulated genes involved in T-cell receptor signaling (TCR), even in absence of surface TCR promoting. Importantly, these genes were also overexpressed in human T-ALL and other STAT5-dependent T-cell cancers. Moreover, human T-ALL cells were sensitive to pharmacologic inhibition by dual STAT3/5 degraders or ZAP70 tyrosine kinase blockers. Thus, we define STAT5 target genes in T-ALL that promote pre-TCR signaling mimicry. We propose therapeutic targeting using selective ZAP70 or STAT3/5 inhibitors in a subgroup of T-ALL patients with prominent IL-7R-JAK1/3-STAT5 activity. Significance We provide detailed functional characterizations of hyperactive STAT5A or STAT5B in thymic T-cell development and transformation. We found that hyperactive STAT5 transcribes T-cell-specific kinases or pre-TCR signaling hubs to promote T-ALL. Biomolecular and next-generation-sequencing methods, transgenesis and pharmacologic interference revealed that hyperactive STAT5 is a key oncogenic driver that can be targeted in T-ALL using STAT3/5 or SYK family member tyrosine kinase inhibitors. Conflict of interest The authors declare no potential conflicts of interest.
Seasonal and daily patterns in known dissolved metabolites in the northwestern Sargasso Sea

Organic carbon in seawater plays a significant role in the global carbon cycle. The concentration and composition of dissolved organic carbon, operationally defined in this project as organic carbon that passes through a 0.2 µm filter, reflect the activity of the biological community and chemical reactions that occur in seawater. From 2016 to 2019, we repeatedly sampled the oligotrophic northwest Sargasso Sea in the vicinity of the Bermuda Atlantic Time-series Study site (BATS) to quantitatively follow known compounds within the pool of dissolved organic matter in the upper 1000 meters of the water column. Dissolved metabolite concentrations revealed patterns with depth and time with most metabolites showing surface enrichment and lower concentrations with increasing depth. Select metabolites displayed seasonal patterns throughout the year, and this seasonality was repeated in each of the years sampled. Concentrations of vitamins, including pantothenic acid (vitamin B5) and riboflavin (vitamin B2), increased annually during winter periods when mixed layer depths were deepest. During diel sampling, light-sensitive riboflavin decreased significantly during daylight hours. Metabolite concentrations over time at BATS showed less variability compared to a previous sample set collected over a broad latitudinal range in the western Atlantic Ocean. The metabolites examined in this study are all components of central carbon metabolism. By examining these metabolites at finer resolution and in a relatively long time series, we have insights into microbial biogeochemical activity, data which are fundamental to understanding the chemical response of marine systems to future changes in climate.
Development of nuclear microsatellite markers in Yerba mate (Ilex paraguariensis St. Hil., Aquifoliaceae Bartl.) from whole-genome sequence data

Ilex paragariensis St. Hil. (yerba mate) (Aquifoliaceae Bartl.) is a plant species with great economic and cultural importance because its leaves are processed and ground to make infusions like mate or tereré. The species is distributed in a continuous area that includes southern Brazil, and part of Paraguay and Argentina. Uruguay represents the southern distribution limit of the species, where small populations can be found as part of riparian forests. Although there are previous reports of molecular markers for this and other species in the genus, the available markers were not informative enough to represent the intra and interpopulation genetic diversity in these marginal populations. In this study, we developed highly informative nuclear polymorphic microsatellite markers to optimize genetic studies in I. paraguariensis. Markers were identified in contigs from the genome sequence of two individuals and then tested for amplification and polymorphism in a diverse panel and at population level. Markers which passed these tests detected levels of heterozygosity similar to those reported for Brazilian populations and great diversity within populations from Uruguay. This set of markers were successfully multiplexed, substantially reducing the costs of the analysis. In combination with previously reported nuclear and plastid markers, they can be used to evaluate the genetic diversity of rear edge populations, identify genotypes for paternity studies and provide relevant information for the conservation and management of germplasm.
Detection of horizontal sequence transfer in microorganisms in the genomic era

Sequence transfer and genome remodeling are very frequent events in microorganisms, especially prokaryotes. This is due to the mosaic structure of the genomes, which calls into question the correct classification of genomes in terms of a single gene or a group of genes. We started here, as a first step, the inventory of bioinformatics tools applied to the detection of horizontal sequence transfers in microorganisms in the genomic era by applying bibliometric survey. Our bibliographic analysis allowed us to identify 17 main tools for the detection of chimeras. The first Bellerophon developed in 2004, followed by CCode and Pintail in 2005; Mallard in 2006; Mothur in 2009; Blackbox Chimera in 2010; Perseus, ChimeraSlayer, UCHIME 1 and UCHIME2, and ChimeraScan in 2011; Decipher in 2012; EBARDenovo and FunFrame in 2013; CATCh in 2015; Uchime 2 in 2016 and ChimeraMiner in April 2019. We then described each of these tools, highlighting their operating principles as well as the advantages and limitations of each (specificities, sensitivity, rapidity and frequent updates). The number of articles citing these tools has increased over the years especially for Mothur, Uchime, VSEARCH and ChimeraSlayer, thus demonstrating the interest of researchers in these tools and the need to decipher chimeras in genomic era.
Colour Difference Assessment in Controlled and Uncontrolled Environments

Two different environments were considered in this study to conduct the psychophysical experiment to find a relationship between the perceived and calculated colour difference in display colours. One of the experiments was in a controlled environment, which took place in the NTNU colour lab using PsychoPy, and the other was conducted online by hosting the same experiment on the Pavlovia website. The experiment was conducted by comparing 48 different colour patches having 6 different color centers. A number of colour difference measurement formulas using different mathematical and statistical methods are introduced on a regular basis by incorporating different concepts. To find the relationship between perceived and computed colour difference, this study used CIEDE2000, CIE94 and CIE76 to calculate the colour difference using formulas. And a category judgment experiment using greyscale anchor point having six categories used for perceived colour difference. There were 17 observers in a controlled environment and 25 observers in an uncontrolled environment experiment without having any colour deficiency problems. The Standard Residual Sum of Squares (STRESS) index was used to find the relationship between the perceived and computed colour difference. Alongside, the STRESS function is also used to test the observers inter and intra observer variation and repeatability. The results show that controlled environment observers achieved a more rational relationship according to the stress index in perceived and computed colour difference using all three formulas. According to the result of inter and intra observer variation, controlled environment observers were more consistent, which archived a lower stress value.
Classification of Spectra from the Infrared Space Observatory PHT-S Database

We have classified over 1500 infrared spectra obtained with the PHT-S spectrometer aboard the Infrared Space Observatory according to the system developed for the Short Wavelength Spectrometer (SWS) spectra by Kraemer et al. The majority of these spectra contribute to subclasses that are either underrepresented in the SWS spectral database or contain sources that are too faint, such as M dwarfs, to have been observed by either the SWS or the Infrared Astronomical Satellite Low Resolution Spectrometer. There is strong overall agreement about the chemistry of objects observed with both instruments. Discrepancies can usually be traced to the different wavelength ranges and sensitivities of the instruments. Finally, a large subset of the observations (≃250 spectra) exhibit a featureless, red continuum that is consistent with emission from zodiacal dust and suggest directions for further analysis of this serendipitous measurement of the zodiacal background.
Flares in Hale 17760 - Magnetic transients in the 1981 July 27 flare

Several magnetic transients were observed in the flare of 1981 July 27 using the vidiomagnetograph at Big Bear Solar Observatory. Images in the Fe I lambda5324 line used by the magnetograph showed emission in the area of the transients. Calculations show that the emission obsrved will explain the magnetic transient features, provided the magnetic field has two components: a strong and a weak or zero field. The elements of each field must be less than 1'' in size, and the strong fiel must occupy less than 20% of the total area.
Optimization of the optical properties of nanostructures through fast numerical approaches

We present an improved and efficient numerical method to determine the optical properties of nanostructures starting from the electronic properties. We study the variation of electronic and optical properties induced by confinement effects in semiconductors quantum objects. We solve the time-independent Schrödinger equation with a new formulation of a shooting method under the effective mass approximation. This formulation is adapted to quantum wells, circular cross-section quantum wires and spherical quantum dots. We applied a correction on the mass to take into account the nonparabolicity of the band structure. The correction gives an accuracy comparable to more demanding calculation methods such as 8-bands k•p, tight binding or even semi-empirical pseudopotential methods. Our results remain valid even for low-bandgap materials and sizes as small as 1 nm. The calculation speed of our method allows optimization procedures that give better understanding of experimental results concerning CdS, CdSe, PbS and PbSe spherical quantum dots. We consider extensive data from the literature. We focus on the relations between the electronic structure and absorption and photoluminescence spectra measured on spin-coated PMMA thin-films containing (core)shell nanoparticles.
Fault detection algorithms for real-time diagnosis in large-scale systems

In this paper, we present a review of different real-time capable algorithms to detect and isolate component failures in large-scale systems in the presence of inaccurate test results. A sequence of imperfect test results (as a row vector of 1's and 0's) are available to the algorithms. In this case, the problem is to recover the uncorrupted test result vector and match it to one of the rows in the test dictionary, which in turn will isolate the faults. In order to recover the uncorrupted test result vector, one needs the accuracy of each test. That is, its detection and false alarm probabilities are required. In this problem, their true values are not known and, therefore, have to be estimated online. Other major aspects in this problem are the large-scale nature and the real-time capability requirement. Test dictionaries of sizes up to 1000 x 1000 are to be handled. That is, results from 1000 tests measuring the state of 1000 components are available. However, at any time, only 10-20% of the test results are available. Then, the objective becomes the real-time fault diagnosis using incomplete and inaccurate test results with online estimation of test accuracies. It should also be noted that the test accuracies can vary with time --- one needs a mechanism to update them after processing each test result vector. Using Qualtech's TEAMS-RT (system simulation and real-time diagnosis tool), we test the performances of 1) TEAMS-RT's built-in diagnosis algorithm, 2) Hamming distance based diagnosis, 3) Maximum Likelihood based diagnosis, and 4) Hidden Markov Model based diagnosis.
City-wide Spatio-temporal Effect on AQI

As the number of people increases, so does the demand of people. In meeting that demand, there is no doubt that mankind is going to face a terrible danger. Where, air pollution plays a significant role for morbidity and mortality. Along with many studies, we have tried highlighting the causes and consequences of air pollution. Our research shows the effect of spatial and temporal patterns on outdoor air quality based on eighteen months of data collected in India. Spatial and temporal correlation with Air Quality Index (AQI) is evaluated using Multiple linear regression and Pearson correlation models. The findings reveal considerable disparity in air pollution levels in India’s three most polluted cities: Chennai, Delhi, Hyderabad, along with Durgapur, our present site of research. To determine relevance and provide a well-established link with AQI, we perform ANOVA test on our spatio-temporal characteristics versus contextual AQI. Additionally, wind direction effects on air quality have been established as an influencing factor.
A CNN Approach To Predicting Non-Invasive Blood Pressure of Surgical Patients

The occurrence of intraoperative hypertension/ hypotension may cause danger to a patient. Therefore, the monitoring of blood pressure change during surgical operation is momentous for anesthetized patient undergoing surgical procedures. The invasive method of measuring arterial blood pressure (ABP) provides accurate and much information, but it requires evaluation by an anesthesiologist and with its long-term use, it also brings a higher risk of infection, and even some patients have pain and discomfort at the catheter placement site after surgery, so it is not suitable for all types of patients. On the other hand, non-invasive method of measuring cuff blood pressure provides little information because of non-continuous measurement. With the emerging of deep learning, there has been more and more discussion on whether non-invasive Photoplethysmography (PPG) can replace invasive ABP as an alternative to continuous BP measurement and even BP prediction. This paper aims to implement a deep learning model to predict SBP/DBP signal by PPG, PPG extended data and Electrocardiography (ECG) data. We trained the CNN-based architecture on preprocessed data including ECG, PPG, 1st and 2nd derivative PPG signal extracted from MIMIC-III(Medical Information Mart for Intensive Care III) waveform database matched subset to predict continuous ABP signals using real world data. The value of SBP and DBP are directly predicted to effectively estimate the accuracy of the predictions. The prediction results fulfill the grade A in British Hypertension Society (BHS) standard and most part of Association for the Advancement of Medical Instrumentation (AAMI)’s standard. The proposed model has been applied for CHANGHUA CHRISTIAN HOSPITAL’s IRB NO:191240. The results depict that our proposed model could effectively predict SBP/DBP signal and be deployed to the operating room realistically.
Torque Enhancement of Surface-mounted Permanent Magnet Synchronous Machines via Axial Assisted Magnets

A torque enhancement scheme using axial assisted magnets for surface-mounted permanent magnet synchronous machines (SPMSMs) is proposed in this paper. It divides the total permanent magnets into two parts viz. main magnets mounted on the rotor surface, and assisted magnets in the axial direction, with the restriction of the same volume of magnets. According to the theoretical derivation and the finite element (FE) analyses, the proposed design can effectively enhance the output torque after a reasonable combination of the size parameters of main and assisted magnets, while the machine outer size, armature winding current, and volume of total permanent magnets are the same as the conventional SPMSM. The optimal results, average torque increased by over 6.2% without sacrificing torque ripple, of the proposed machine are obtained with the sequential optimization and validated by the experiments.
Networked Control of Distributed Energy Systems in Dispatchable Microgrids: System Modeling and Stability Considerations

Inverter-interfaced distributed energy systems have been spreading over low-voltage electric grids to achieve higher integration of renewable sources while offering adjustable controllability over power conversion. In addition, due to their remote control capabilities that support a networked system framework, such inverters play an essential role from the perspective of dispatchable microgrids. These are power systems of limited size incorporating information and communication technology infrastructures. By managing network-controlled inverters, it is possible to regulate the power dispatchability of microgrids, allowing them to flexibly exchange power with the upstream grid as needed flexibly. Nonetheless, the control modeling and stability concerns of inverters forming a networked system within such a perspective lack discussion in the literature. Hence, this paper proposes a generic system model for a dispatchable microgrid, considering that a central controller steers inverters under a networked control framework. Moreover, stability considerations are presented, highlighting the impact of communication delays on the microgrid operation and indicating that multiple aspects still need to be investigated in future research.
Wave number determination of Pc 1–2 mantle waves considering He++ ions: A Cluster study

The present case study concerns narrowband electromagnetic emission detected in the distant cusp region simultaneously with upgoing plasma flows. The wave properties match the usual properties of the Pc 1–2 mantle waves: small angle between the wave vector and the magnetic field line, left‐hand polarization, and propagation toward the ionosphere. We report here the first direct wave vector measurement of these waves (about 1.2 × 10− 2 rad/km) through multi spacecraft analysis using the three magnetic components and, at the same time, through single spacecraft analysis based on the refractive index analysis using the three magnetic components and two electric components. The refractive index analysis offers a simple way to estimate wave numbers in this frequency range. Numerical calculations are performed under the observed plasma conditions. The obtained results show that the ion distribution functions are unstable to ion cyclotron instability at the observed wave vector value, due to the large ion temperature anisotropy. We thus show that these electromagnetic ion cyclotron (EMIC) waves are amplified in the distant cusp region. The Poynting flux of the waves is counterstreaming with respect to the plasma flow. This sense of propagation is consistent with the time necessary to amplify the emissions to the observed level. We point out the role of the wave damping at the He++ gyrofrequency to explain that such waves cannot be observed from the ground at the cusp foot print location.
Leaf Area Index Specification for Use in Mesoscale Weather Prediction Systems

Abstract The energy budget at the surface is strongly influenced by the presence of vegetation, which alters the partitioning of thermal energy between sensible and latent heat fluxes. Despite its relevance, numerical weather prediction (NWP) systems often use only two parameters to describe the vegetation cover: the fractional area of vegetation occupying a given pixel and the leaf area index (LAI). In this study, the Consortium for Small-Scale Modelling (COSMO) limited-area forecast model is used to investigate the sensitivity of regional predictions to LAI assumptions over the Italian peninsula. Three different approaches are compared: a space- and time-invariant LAI dataset, a LAI specification based on Coordination of Information on the Environment (CORINE) land classes, and a Moderate Resolution Imaging Spectroradiometer (MODIS) satellite-retrieved dataset. The three approaches resolve increasingly higher moments both in time and space of LAI probability density functions. Forecast scores employing .
Higher dimensional bright solitons and their collisions in a multicomponent long wave–short wave system

Bright plane soliton solutions of an integrable (2+1)-dimensional (n + 1)-wave system are obtained by applying Hirota's bilinearization method. First, the soliton solutions of a three-wave system consisting of two short-wave components and one long-wave component are found and then the results are generalized to the corresponding integrable (n + 1)-wave system with n short waves and a single long wave. It is shown that the solitons in the short-wave components (say S(1) and S(2)) can be amplified by merely reducing the pulse width of the long-wave component (say L). Study of the collision dynamics reveals some interesting behaviour: the solitons which split up in the short-wave components undergo shape changing collisions with intensity redistribution and amplitude-dependent phase shifts. Even though a similar type of collision is possible in (1+1)-dimensional multicomponent integrable systems, to our knowledge we report this kind of collision in (2+1) dimensions for the first time. However, solitons which appear in the long-wave component exhibit only elastic collision though they undergo amplitude-dependent phase shifts.