Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of emissions from biomass burning in China (2003–2017) based on MODIS fire radiative energy data

Abstract. Biomass burning plays a significant role in air pollution and climate change. In this study, we used a method based on fire radiative energy (FRE) to develop a biomass burning emission inventory for China from 2003 to 2017. Daily fire radiative power (FRP) data derived from 1 km MODIS Thermal Anomalies/Fire products (MOD14/MYD14) were used to calculate FRE and combusted biomass. Available emission factors were assigned to four biomass burning types: forest, cropland, grassland, and shrubland fires. The farming system and crop types in different temperate zones were taken into account in this research. Compared with traditional methods, the FRE method was found to provide a more reasonable estimate of emissions from small fires. The estimated average annual emission ranges, with a 90 % confidence interval, were 91.4 (72.7–108.8) Tg CO2 yr−1, 5.0 (2.3–7.8) Tg CO yr−1, 0.24 (0.05–0.48) Tg CH4 yr−1, 1.43 (0.53–2.35) Tg NMHC yr−1, 0.23 (0.05–0.45) Tg NOx yr−1, 0.09 (0.02–0.17) Tg NH3 yr−1, 0.03 (0.01–0.05) Tg SO2 yr−1, 0.04 (0.01–0.08) Tg BC yr−1, 0.27 (0.07–0.49) Tg OC yr−1, 0.51 (0.19–0.84) Tg PM2.5 yr−1, 0.57 (0.15–1.05) Tg PM10 yr−1, where NMHC, BC, and OC are nonmethane hydrocarbons, black carbon, and organic carbon, respectively. Forest fires are determined to be the primary contributor to open fire emissions, accounting for 45 % of the total CO2 emissions (average 40.8 Tg yr−1). Crop residue burning ranked second place with a large portion of 39 % (average 35.3 Tg yr−1). During the study period, emissions from forest and grassland fires showed a significant downward trend. Crop residue emissions continued to rise during 2003–2015 but dropped by 42 % in 2015–2016. Emissions from shrubland were negligible and little changed. Forest and grassland fires are concentrated in northeastern China and southern China, especially in the dry season (from October to March of the following year). Plain areas with high crop yields, such as the North China Plain, experienced high agricultural fire emissions in harvest seasons. Most shrubland fires were located in Yunnan and Guangdong provinces. The resolution of our inventory (daily, 1 km) is much higher than previous inventories, such as GFED4s and GFASv1.0. It could be used in global and regional air quality modeling.
A Efficiently Deciding μ-calculus with Converse over Finite Trees

We present a sound and complete satisfiability-testing algorithm and its effective implementation for an alternation-free modal μ-calculus with converse, where formulas are cycle-free, and which is interpreted over finite ordered trees. The time complexity of the satisfiability-testing algorithm is 2O(n) in terms of formula size n. The algorithm is implemented using symbolic techniques (BDD). We present crucial implementation techniques and heuristics that we used to make the algorithm as fast as possible in practice. Our implementation is available online, and can be used to solve logical formulas of practically significant size.
Neurotransmitter signaling specifies sweat gland stem cell fate through SLN-mediated intracellular calcium regulation

Sympathetic nerves co-develop with their target organs and release neurotransmitters to stimulate their functions after maturation. Here, we provide the molecular mechanism that during sweat gland morphogenesis, neurotransmitters released from sympathetic nerves act first to promote sweat duct elongation via norepinephrine and followed by acetylcholine to specify sweat gland stem cell fate, which matches the sequence of neurotransmitter switch. Without neuronal signals during development, the basal cells switch to exhibit suprabasal (luminal) cell features. Sarcolipin (SLN), a key regulator of sarcoendoplasmic reticulum (SR) Ca2+-ATPase (SERCA), expression is significantly down-regulated in the sweat gland myoepithelial cells upon denervation. Loss of SLN in sweat gland myoepithelial cells leads to decreased intracellular Ca2+ over time in response to ACh stimulation, as well as upregulation of luminal cell features. In cell culture experiments, we showed that contrary to the paradigm that elevation of Ca2+ promote epidermal differentiation, specification of the glandular myoepithelial (basal) cells requires high Ca2+ while lowering Ca2+ level promotes luminal (suprabasal) cell fate. Our work highlights that neuronal signals not only act transiently for mature sweat glands to function, but also exert long-term impact on glandular stem cell specification through regulating intracellular Ca2+ dynamics.
Rat movements reflect internal decision dynamics in an evidence accumulation task

Perceptual decision-making involves multiple cognitive processes, including accumulation of sensory evidence, planning, and executing a motor action. How these processes are intertwined is unclear; some models assume that decision-related processes precede motor execution, whereas others propose that movements reflecting on-going decision processes occur before commitment to a choice. Here we develop and apply two complementary methods to study the relationship between decision processes and the movements leading up to a choice. The first is a free response pulse-based evidence accumulation task, in which stimuli continue until choice is reported. The second is a motion-based drift diffusion model (mDDM), in which movement variables from video pose estimation constrain decision parameters on a trial-by-trial basis. We find the mDDM provides a better model fit to rats’ decisions in the free response accumulation task than traditional DDM models. Interestingly, on each trial we observed a period of time, prior to choice, that was characterized by head immobility. The length of this period was positively correlated with the rats’ decision bounds and stimuli presented during this period had the greatest impact on choice. Together these results support a model in which internal decision dynamics are reflected in movements and demonstrate that inclusion of movement parameters improves the performance of diffusion-to-bound decision models. Highlights Development and validation of a free response pulse-based accumulation task for rats Response times are well described by drift diffusion models Incorporating movement data into diffusion models improves inference of latent decisions variables Rats weight sensory evidence most strongly prior to movement
Microbial metabolic potential of hydrothermal vent chimneys along the Submarine Ring of Fire

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world’s oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic for each of these hydrothermal vent chimneys, as well as highlighting differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents. DNA from the chimneys was sequenced, assembled into contigs, annotated for gene function, and binned into metagenome-assembled genomes, or MAGs. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolism were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa had an overlap of these metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with low carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found to be at higher abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered. IMPORTANCE The metabolic byproducts of microorganisms that form and reside in hydrothermal vent chimneys facilitate nutrient cycling in both the hydrothermal vent ecosystem and throughout the world’s oceans. Diverse communities of microbes utilize chemicals in the venting fluid to gain energy and biomass. Here, metagenomic and amplicon sequencing was used to identify metabolism genes to better understand the metabolic potential of chimneys. The combination of genes detected in this study sheds light on hydrothermal vent chimneys’ community structure and metabolic potential throughout the Pacific Ocean.
Stress-sensitive inference of task controllability

Estimating the controllability of the environment enables agents to better predict upcoming events and decide when to engage controlled action selection. How does the human brain estimate controllability? Trial-by-trial analysis of choices, decision times, and neural activity in an explore-and-predict task demonstrate that humans solve this problem by comparing the predictions of an “actor” model with those of a reduced “spectator” model of their environment. Neural BOLD responses within striatal and medial prefrontal areas tracked the instantaneous difference in the prediction errors generated by these two statistical learning models. BOLD activity in the posterior cingulate, temporoparietal, and prefrontal cortices covaried with changes in estimated controllability. Exposure to inescapable stressors biased controllability estimates downward and increased reliance on the spectator model in an anxiety-dependent fashion. Taken together, these findings provide a mechanistic account of controllability inference and its distortion by stress exposure.
Investigating the impact of on-chip interconnection noise on dynamic thermal management efficiency

Dynamic Thermal Management (DTM) emerged as a solution to address the reliability challenges with thermal hotspots and unbalanced temperatures. DTM efficiency is highly affected by the accuracy of the temperature information presented to the DTM manager. This work aims to investigate the effect of inaccuracy caused by the deep sub-micron (DSM) noise during the transmission of temperature information to the manager on DTM efficiency. A simulation framework has been developed and results show up to 62% DTM performance degradation under DSM noise. The finding highlights the importance of further research in providing reliable on-chip data transmission in DTM application.
Unraveling Neural Complexity: Exploring Brain Entropy to Yield Mechanistic Insight in Neuromodulation Therapies for Tobacco Use Disorder

Neuromodulation therapies, such as repetitive transcranial magnetic stimulation (rTMS), have shown promise as treatments for tobacco use disorder (TUD). However, the underlying mechanisms of these therapies remain unclear, which may hamper optimization and personalization efforts. In this study, we investigated alteration of brain entropy as a potential mechanism underlying the neural effects of noninvasive brain stimulation by rTMS in people with TUD. We employed sample entropy (SampEn) to quantify the complexity and predictability of brain activity measured using resting-state fMRI data. Our study design included a randomized single-blind study with 42 participants who underwent 2 data collection sessions. During each session, participants received high-frequency (10Hz) stimulation to the dorsolateral prefrontal cortex (dlPFC) or a control region (visual cortex), and resting-state fMRI scans were acquired before and after rTMS. Our findings revealed that individuals who smoke exhibited higher baseline SampEn throughout the brain as compared to previously-published SampEn measurements in control participants. Furthermore, high-frequency rTMS to the dlPFC but not the control region reduced SampEn in the insula and dlPFC, regions implicated in TUD, and also reduced self-reported cigarette craving. These results suggest that brain entropy may serve as a potential biomarker for effects of rTMS, and provide insight into the neural mechanisms underlying rTMS effects on smoking cessation. Our study contributes to the growing understanding of brain-based interventions for TUD by highlighting the relevance of brain entropy in characterizing neural activity patterns associated with smoking. The observed reductions in entropy following dlPFC-targeted rTMS suggest a potential mechanism for the therapeutic effects of this intervention. These findings support the use of neuroimaging techniques to investigate the use of neuromodulation therapies for TUD.
Active tectonic blocks and strong earthquakes in the continent of China

The primary pattern of the late Cenozoic to the present tectonic deformation of China is characterized by relative movements and interactions of tectonic blocks. Active tectonic blocks are geological units that have been separated from each other by active tectonic zones. Boundaries between blocks are the highest gradient of differential movement. Most of tectonic activity occurs on boundaries of the blocks. Earthquakes are results of abrupt releases of accumulated strain energy that reaches the threshold of strength of the earth’s crust. Boundaries of tectonic blocks are the locations of most discontinuous deformation and highest gradient of stress accumulation, thus are the most likely places for strain energy accumulation and releases, and in turn, devastating earthquakes. Almost all earthquakes of magnitude greater than 8 and 80%–90% of earthquakes of magnitude over 7 occur along boundaries of active tectonic blocks. This fact indicates that differential movements and interactions of active tectonic blocks are the primary mechanism for the occurrences of devastating earthquakes.
Screening and monitoring of the BTKC481S mutation in a real‐world cohort of patients with relapsed/refractory chronic lymphocytic leukaemia during ibrutinib therapy

The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has revolutionised the therapeutic landscape of chronic lymphocytic leukaemia (CLL). Acquired mutations emerging at position C481 in the BTK tyrosine kinase domain are the predominant genetic alterations associated with secondary ibrutinib resistance. To assess the correlation between disease progression, and the emergence and temporal dynamics of the most common resistance mutation BTKC481S, sensitive (10−4) time‐resolved screening was performed in 83 relapsed/refractory CLL patients during single‐agent ibrutinib treatment. With a median follow‐up time of 40 months, BTKC481S was detected in 48·2% (40/83) of the patients, with 80·0% (32/40) of them showing disease progression during the examined period. In these 32 cases, representing 72·7% (32/44) of all patients experiencing relapse, emergence of the BTKC481S mutation preceded the symptoms of clinical relapse with a median of nine months. Subsequent Bcl‐2 inhibition therapy applied in 28/32 patients harbouring BTKC481S and progressing on ibrutinib conferred clinical and molecular remission across the patients. Our study demonstrates the clinical value of sensitive BTKC481S monitoring with the largest longitudinally analysed real‐world patient cohort reported to date and validates the feasibility of an early prediction of relapse in the majority of ibrutinib‐treated relapsed/refractory CLL patients experiencing disease progression.
Edinburgh’s Syntax-Based Systems at WMT 2015

This paper describes the string-to-tree systems built at the University of Edinburgh for the WMT 2014 shared translation task. We developed systems for English-German, Czech-English, FrenchEnglish, German-English, Hindi-English, and Russian-English. This year we improved our English-German system through target-side compound splitting, morphosyntactic constraints, and refinements to parse tree annotation; we addressed the out-of-vocabulary problem using transliteration for Hindi and Russian and using morphological reduction for Russian; we improved our GermanEnglish system through tree binarization; and we reduced system development time by filtering the tuning sets.
Aalborg Universitet Using a Graphics Turing Test to Evaluate the Effect of Frame Rate and Motion Blur on Telepresence of Animated Objects

A limited Graphics Turing Test is used to determine the frame rate that is requ ired to achieve telepresence of an animated object. For low object velocities of 2.25 and 4.5 degrees of v i ual angle per second at 60 frames per second a rotating object with no added motion blur is able to pass the test. T h results of the experiments confirm previous results in psychophysics and show that the Graphics T uring Test is a useful tool in computer graphics. Even with simulated motion blur, our Graphics Turing Test could not be passed with frame rates of 30 and 20 frames per second. Our results suggest that 60 frames pe r second (instead of 30 frames per second) should be considered the minimum frame rate to achieve object telepresen ce and that motion blur provides only limited benefits.
NUMERICAL SIMULATION OF THE TWO-DIMENSIONAL INCOMPRESSIBLE FLOW AROUND ELLIPTIC CYLINDERS USING THE VORTEX METHOD

Abstract. The study of external incompressible flows at high Reynolds numbers around bluff bodies finds extensive applicability to real-life problems, in addition to the scientific interest as a means for testing numerical algorithms. For a wide range of Reynolds numbers such flows are characterized by the formation of a Von Karman-type periodic wake. The occurrence of flow separation makes the prediction of these flows very difficult, and one has to rely on experimental data to calculate the aerodynamic forces on the body. Many attempts to numerically simulate the flow details have been reported in the literature, and a variety of both mesh-based and mesh-free methods have been used. In this paper we use a new mesh-free two-dimensional discrete vortex method to simulate the high Reynolds number flow around an elliptic cylinder. Lamb vortices are generated along the cylinder surface, whose strengths are determined to ensure that the no-slip condition is satisfied and that circulation is conserved. The impermeability condition is imposed through the application of a source panel method, so that mass conservation is explicitly enforced. The dynamics of the body wake is computed using the convection-diffusion splitting algorithm, where the diffusion process is simulated using the random walk method, and the convection process is carried out with a lagrangian first-order time-marching scheme. Results for the time history of the lift and drag coefficients as well as pressure coefficient distribution on the body surface are presented and compared to other results available in the literature.
Stock Market Volatility and Learning

Introducing bounded rationality into a standard consumption based asset pricing model with a representative agent and time separable preferences strongly improves empirical performance. Learning causes momentum and mean reversion of returns and thereby excess volatility, persistence of price-dividend ratios, long-horizon return predictability and a risk premium, as in the habit model of Campbell and Cochrane (1999), but for lower risk aversion. This is obtained, even though we restrict consideration to learning schemes that imply only small deviations from full rationality. The findings are robust to the particular learning rule used and the value chosen for the single free parameter introduced by learning, provided agents forecast future stock prices using past information on prices.
A Single-Cell Level Comparison of Human Inner Ear Organoids and the Human Cochlea and Vestibular Organs

Genetic inner ear disorders are among the most common congenital abnormalities and lead to hearing loss and balance disorders. Ideally, tissue culture models of the inner ear should contain a functional unit combining otic sensory and nonsensory cell types to recapitulate the varied etiologies of inner ear disorders. Here, we evaluated cell type diversity of late-stage human pluripotent stem cell-derived inner ear organoids using single-cell transcriptomic analysis, electron microscopy and immunohistochemistry. We observed the induction of on-target inner ear-related periotic mesenchymal cells alongside off-target induction of skeletal myocytes, endothelial cells, and ependymal cells. By constructing a single-cell transcriptomic atlas of the human fetal and adult inner ear, we show that epithelium in the inner ear organoids contains cochlear and vestibular identities similar to the developing human inner ear. Moreover, the inner ear organoids contain immature type I and type II vestibular hair cells. Within these putative inner ear cell types, we confirmed the expression of genes and proteins linked to sensorineural hearing loss. This approach using human inner ear organoids would allow for disease modeling of specific genetic inner ear pathologies in the sensory and nonsensory domains of the inner ear.
University of Groningen An experimental evaluation of a loop versus a reference design for two-channel microarrays

Motivation: Despite theoretical arguments that so-called ‘loop designs’ for two-channel DNA microarray experiments are more efficient, biologists continue to use ‘reference designs’. We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicolor ). In each case, both a loop and a reference design were used with the same RNA preparations with the aim of studying their relative efficiency. Results: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example, by taking log-ratios or including spot effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice. Availability: The data and R code are available at http://exgen. ma.umist. ac.uk Contact: veronica.vinciotti@brunel.ac.uk
CIGB-300 synthetic peptide, an antagonist of CK2 kinase activity, as a treatment for Covid-19. A computational biology approach

Drug repositioning became the first choice for treating Covid-19 patients due to the urgent need to deal with the pandemic. Similarities in the hijacking mechanisms used by SARS-CoV-2 and several type of cancer, suggest the repurposing of cancer drugs to treat Covid-19. CK2 kinase antagonists have been proposed for the treatment of cancer. A recent study in cells infected with SARS-CoV-2 virus found a significant CK2 kinase activity, and the use of a CK2 inhibitor showed antiviral responses. CIGB-300, originally designed as an anticancer peptide, is an antagonist of CK2 kinase activity that binds to CK2 phospho-acceptor sites. Recent preliminary results show an antiviral activity of CIGB-300 versus a surrogate model of coronavirus. Here we present a computational biology study that provides evidences at the molecular level of how CIGB-300 might interfere with SARS-CoV-2 life cycle inside infected human cells. First, from SARS-CoV studies, we infer the potential incidence of CIGB-300 in SARS-CoV-2 interference on immune response. Next, from the analysis of multiple Omics data, we propose the action of CIGB-300 since early stage of viral infections perturbing the virus hijacking of RNA splicing machinery. It was also predicted the interference of CIGB-300 in virus-host interactions responsible for the high infectivity and the particular immune response to SARS-CoV-2 infection. Further, we provide evidences of CIGB-300 attenuation of phenotypes related to muscle, bleeding, coagulation and respiratory disorders.