Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression and processing of polycistronic artificial microRNAs and trans-acting siRNAs in Solanum lycopersicum and Nicotiana benthamiana

Targeted gene silencing using small regulatory RNAs is a widely used technique for genetic studies in plants. Artificial microRNAs are one common approach; they have the advantage of producing just a single functional small RNA which can be designed for high target specificity and low off-target effects. Simultaneous silencing of multiple targets with artificial microRNAs can be achieved by producing polycistronic microRNA precursors. Alternatively, specialized trans-acting short interfering RNA (tasiRNA) precursors can be designed to produce several specific tasiRNAs at once. Here we tested several artificial microRNA- and tasiRNA-based methods for multiplexed gene silencing in Solanum lycopersicum (tomato) and Nicotiana benthamiana. Small RNA sequencing analyses revealed that many previously described approaches resulted in poor small RNA processing. The 5’-most microRNA precursor hairpins on polycistronic artificial microRNA precursors were generally processed more accurately than precursors at the 3’ end. Polycistronic artificial microRNAs where the hairpin precursors were separated by transfer RNAs had the best processing precision. Strikingly, artificial tasiRNA precursors failed to be processed in the expected phased manner in our system. These results highlight the need for further development of multiplexed artificial microRNA and tasiRNA strategies. The importance of small RNA sequencing, as opposed to single-target assays such as RNA blots or real-time PCR, is also discussed. Significance statement Several strategies for multiplexed gene silencing using artificial microRNAs or tasiRNAs have been described. We find that many result in imprecise processing, and thus low accumulation of the intended small RNAs. Our findings highlight the importance of small RNA sequencing to fully analyze gene silencing experiments, and also the need for continued methodological development of these methods.
A molecular dynamics study of the atomic structure of (CaO)x(Al2O3)1−x glass with x = 0.625 close to the eutectic

Aluminate glasses are difficult to prepare as they do not contain traditional network formers, but they are promising materials for optical applications. The atomic structure of calcium aluminate glasses has been studied using several experimental techniques. The current study uses molecular dynamics to obtain a model of a (CaO)0.625(Al2O3)0.375 glass close to the eutectic. The glass consists of a tetrahedral alumina network with average network polymerization of n = 3.3. Ca acts as a network modifier with average coordination of 6.2. Ca is typically coordinated to three bridging oxygens (Ob) and three non-bridging oxygens (Onb), with Ca–Onb bonds noticeably shorter than the Ca–Ob bonds. A new method of analysing modifier cation coordination is presented, which specifically shows the distribution of Ca coordination NCaO in terms of combinations of NCaOb and NCaOnb. Ob is most often coordinated to two Al plus two Ca, and Onb is most often coordinated to one Al plus three Ca. The typical coordinations of Ca, Ob, and Onb all have a noticeable similarity to those for the 5CaO·3Al2O3 crystal. The Ca–Ca distribution shows a clear similarity to that for (CaO)0.5(SiO2)0.5 glass, and this is attributed to the equal atomic number densities of Ca in these glasses.
The Quest for Covert Consciousness

Plato, in his Allegory of the Cave, contemplates a group of people who have lived their entire lives facing a wall of a cave and whose impressions of the world are constrained to perceptual experiences of shadows cast on the wall by entities that are never directly observed. Since time immemorial, conscious states of others have been like Platonic shadows, inferred only imperfectly and indirectly through close observation of behaviors. Although for centuries philosophers and neuroscientists have sought to bring us closer to understanding consciousness, an influx of neurotechnologies now enables clinicians and researchers to potentially improve detection of consciousness and prediction of its recovery.1 Innovations in neuroimaging and electrophysiologic techniques now may permit detection of states of consciousness not readily discernible by bedside examination, known as covert consciousness or cognitive motor dissociation.2 The discovery of covert consciousness raises distinctive issues surrounding both the diagnosis and prognosis of persons with disorders of consciousness (DoC), highlighting the need for caution during the acute phase of neuroprognostication and exposing gaps in knowledge about the epidemiology and phenomenology of covert consciousness. These innovations represent a possible step forward from philosophical and scientific traditions that relied on behavioral observations to detect consciousness. In turn, these breakthroughs prompt reconsideration of standard approaches to the evaluation of persons with DoC and necessitate appraisal of how clinicians should communicate results of novel techniques with indeterminate meanings to surrogates. Proactive integration of neuroethical insights in clarifying responsible ends to which these technologies should be directed is essential for addressing these timely challenges. This article proposes an ethical framework to help the clinical and research community consider how to use these emerging neurotechnologies responsibly, calls for careful consideration of the consequences of searching for covert consciousness in practice, and highlights critical avenues for further study of how the finding of covert consciousness might help predict goal-concordant functional recovery.
Gas-Phase Redox Dynamics in High-Energy Collisions

Mass analysed ion kinetic energy (MIKE) spectra following collisions have been recorded using a double focusing mass spectrometer with 5 kV acceleration voltage. Metal complexes studied were formed by pick-up of metal atoms in mixed argon/solvent clusters made by supersonic expansion. DFT calculations were used to rationalise experimental data. Complexes of the form MLn+ where M = Mg, Ca, Mn, Cu, and Zn while L = NH3, CO2, benzene, pyridine, acetonitrile, and acetone have been collided with O2 and MgLn+ also with CO2, N2O, acetonitrile, and benzene. Complexes with few ligands are the most prone to oxidation due to their high speed which facilitates electron transfer. Calculated electron affinities, Mulliken populations, and natural bond orbitals of collision gases were used to rationalise electron transfer trends. Collision gases trap electrons more efficiently if they have π-bonds or adjacent electronegative atoms. Metal complex and molecular dications were collided with H2 and O2 to determine the stability of their reduced products. No systematic differences were found between collisions with the two gases at the collision energies examined. The fate of monocations formed in collision depends on their relaxation energy and the dissociation energy of relaxed monocations. LZ theory was unable to explain MIKE spectra. Metal complexes MLn+ and MLn2+ were collided with O2 to determine the propensity to form MXLn-m+ where M = Mg, Ca, Mn, Cu, and Zn while L = CH3X with X = F and Cl. Reactivity is determined by the IE of MLn+ which decrease with increasing n. Dications due to their high dissociation energy are much more likely to react as they can have enough internal energy to overcome potential barriers.
Re-membering HIV in the Black Church: women’s religious and social identity in relation to perceived risk and men on the down low

Abstract This analysis of 84 interviews with female Black Church leaders and members from Atlanta, GA, examined how women in Black churches construct definitions of, and identities in relation to, HIV narratives about men on the down low. We analyse these narratives as collective memories, through the theoretical lens of memory and trauma studies, by identifying how women understand themselves as the victims of men on the down low transmitting HIV; describe this as a painful experience; make public claims about this experience; and draw on theological understandings to make these claims. The narratives articulate how Black communal modes of meaning making have been disrupted by the HIV epidemic and assign responsibility for HIV transmission to men on the down low, who are perceived to be engaged in risky sexual behaviour. We discuss these results in relation to HIV education and prevention and suggest health educators can engage Black church leaders by understanding these narratives as forms of countermemory.
Neddylation stabilizes Nav1.1 to maintain interneuron excitability and prevent seizures in murine epilepsy models.

The excitability of interneurons requires Nav1.1, the α subunit of voltage-gated sodium channel. Nav1.1 deficiency and mutations reduce interneuron excitability, a major pathological mechanism for epilepsy syndromes. However, the regulatory mechanisms of Nav1.1 expression remain unclear. Here we provide evidence that neddylation is critical to Nav1.1 stability. Mutant mice lacking Nae1, an obligatory component of the E1 ligase for neddylation, in parvalbumin-positive interneurons (PVINs) exhibited spontaneous epileptic seizures and premature death. Electrophysiological studies indicate that Nae1 deletion reduced in PVIN excitability and GABA release, and consequently increased the network excitability of pyramidal neurons (PyNs). Further analysis revealed a reduction in sodium current density, not a change in channel property, in mutant PVINs and decreased Nav1.1 protein level. These results suggest that insufficient neddylation in PVINs reduces Nav1.1 stability and thus the excitability of PVINs; ensuing increased PyN activity causes seizures in mice. In agreement, Nav1.1 was found reduced by proteomic analysis that revealed abnormality in synapses and metabolic pathways. Our findings, for the first time, described a role of neddylation in maintaining Nav1.1 stability for PVIN excitability and reveal a new mechanism in pathogenesis of epilepsy.
Identification and characterization of sex‐biased and differentially expressed miRNAs in gonadal developments of the Chinese mitten crab, Eriocheir sinensis

MicroRNA (miRNA) is a posttranscriptional downregulator that plays a vital role in a wide variety of biological processes. In this study, we constructed five ovarian and testicular small RNA libraries using two somatic libraries as reference controls for the identification of sex‐biased miRNAs and gonadal differentially expressed miRNAs (DEMs) of the Chinese mitten crab, Eriocheir sinensis. A total of 535 known and 243 novel miRNAs were identified, including 312 sex‐biased miRNAs and 402 gonadal DEMs. KEGG pathway analysis showed that DEM target genes were statistically enriched in MAPK, Wnt, and GnRH signaling pathway, and so on. A number of the sex‐biased miRNAs target genes associated with sex determination/differentiation, such as IAG, Dsx, Dmrt1, and Fem1, while others target the genes related to gonadal development, such as P450s, Wnt, Ef1, and Tra‐2c. Dual‐luciferase reporter assay in vitro further confirmed that miR‐34 and let‐7b can downregulate IAG expression, miR‐9‐5p, let‐7d, let‐7b, and miR‐8915 can downregulate Dsx. Taken together, these data strongly suggest a potential role for the sex‐biased miRNAs in sex determination/differentiation and gonadal development in the crab.
Pressure and Temperature Dependence of Local Structure and Dynamics in an Ionic Liquid

A detailed understanding of the local dynamics in ionic liquids remains an important aspect in the design of new ionic liquids as advanced functional fluids. Here, we use small-angle X-ray scattering and quasi-elastic neutron spectroscopy to investigate the local structure and dynamics in a model ionic liquid as a function of temperature and pressure, with a particular focus on state points (P,T) where the macroscopic dynamics, i.e., conductivity, is the same. Our results suggest that the initial step of ion transport is a confined diffusion process, on the nanosecond timescale, where the motion is restricted by a cage of nearest neighbors. This process is invariant considering timescale, geometry, and the participation ratio, at state points of constant conductivity, i.e., state points of isoconductivity. The connection to the nearest-neighbor structure is underlined by the invariance of the peak in the structure factor corresponding to nearest-neighbor correlations. At shorter timescales, picoseconds, two localized relaxation processes of the cation can be observed, which are not directly linked to ion transport. However, these processes also show invariance at isoconductivity. This points to that the overall energy landscape in ionic liquids responds in the same way to density changes and is mainly governed by the nearest-neighbor interactions.
Azido-1,2,5-oxadiazoles in reactions with 1,3-dicarbonyl compounds

The 1,3-dipolar cycloaddition of azido-1,2,5-oxadiazoles (azidofurazans) to dicarbonyl compounds was studied, and a new procedure for the synthesis of 4-R-3-(4-R1-5-R2-1,2,3-triazol-1-yl)-1,2,5-oxadiazoles was proposed.
Automatic 3D adaptive vessel segmentation based on linear relationship between intensity and complex-decorrelation in optical coherence tomography angiography.

Background Vascular quantitative metrics have been widely used in the preclinical studies and clinical applications (e.g., the diagnosis and treatment of port wine stain, PWS), which require accurate vessel segmentation. An automatic 3D adaptive vessel segmentation is in need for a reproducible and objective quantification of the optical coherence tomography angiography (OCTA) image. Methods Human skin imaging was performed with a lab-built optical coherence tomography (OCT) system. Rather than separately applying the conventional 2-step (intensity and binarization) thresholding in the decorrelation-contrast OCTA, we proposed a 3D adaptive threshold using the linear relationship between the local intensity and complex-decorrelation which was termed as inverse SNR-decorrelation (ID) threshold. Furthermore, the ID threshold was automatically determined by defining a binary image similarity (BISIM) index as the feedback and searching the ID threshold with the minimal BISIM value. The proposed ID-BISIM threshold was applied to the acquired OCTA skin images for further vessel quantification. Results The proposed ID-BISIM threshold enabled a 3D adaptive binarization and presented superior sensitivity and specificity in vessel segmentation over conventional 2-step thresholding method in the decorrelation-contrast OCTA and a 37-65% improvement of the Youden's index in human skin experiments. The 3D binarization enabled a depth-resolved vessel skeleton and enhanced the differentiation of the overlapping vessels in the depth direction. Using ID-BISIM, the quantitative OCTA image presented a significant increase of vessel diameter index (P=0.0015) and vessel area density (VAD) (P=0.0485) as well as a significant decrease of vessel complexity index (VCI) (P=0.0094) in PWS lesion skin compared with normal skin. Conclusions The proposed ID-BISIM method enables an automatic 3D adaptive vessel segmentation with enhanced performance in quantitative OCTA. The vascular quantitative metrics would be a useful tool for improving the diagnosis and the treatment of PWS.
Anoctamin 2-chloride channels reduce simple spike activity and mediate inhibition at elevated calcium concentration in cerebellar Purkinje cells

Modulation of neuronal excitability is a prominent way of shaping the activity of neuronal networks. Recent studies highlight the role of calcium-activated chloride currents in this context, as they can both increase or decrease excitability. The calcium-activated chloride channel Anoctamin 2 (ANO2 alias TMEM16B) has been described in several regions of the mouse brain, including the olivo-cerebellar system. In inferior olivary neurons, ANO2 was proposed to increase excitability by facilitating the generation of high-threshold calcium spikes. An expression of ANO2 in cerebellar Purkinje cells was suggested, but its role in these neurons remains unclear. In the present study, we confirmed the expression of Ano2 mRNA in Purkinje cells and performed electrophysiological recordings to examine the influence of ANO2-chloride channels on the excitability of Purkinje cells by comparing wildtype mice to mice lacking ANO2. Recordings were performed in acute cerebellar slices of adult mice, which provided the possibility to study the role of ANO2 within the cerebellar cortex. Purkinje cells were uncoupled from climbing fiber input to assess specifically the effect of ANO2 channels on Purkinje cell activity. We identified an attenuating effect of ANO2-mediated chloride currents on the instantaneous simple spike activity both during strong current injections and during current injections close to the simple spike threshold. Moreover, we report a reduction of inhibitory currents from GABAergic interneurons upon depolarization, lasting for several seconds. Together with the role of ANO2-chloride channels in inferior olivary neurons, our data extend the evidence for a role of chloride-dependent modulation in the olivo-cerebellar system that might be important for proper cerebellum-dependent motor coordination and learning.
An Integrated Reinforcement Learning and Centralized Programming Approach for Online Taxi Dispatching

Balancing the supply and demand for ride-sourcing companies is a challenging issue, especially with real-time requests and stochastic traffic conditions of large-scale congested road networks. To tackle this challenge, this article proposes a robust and scalable approach that integrates reinforcement learning (RL) and a centralized programming (CP) structure to promote real-time taxi operations. Both real-time order matching decisions and vehicle relocation decisions at the microscopic network scale are integrated within a Markov decision process framework. The RL component learns the decomposed state-value function, which represents the taxi drivers’ experience, the off-line historical demand pattern, and the traffic network congestion. The CP component plans nonmyopic decisions for drivers collectively under the prescribed system constraints to explicitly realize cooperation. Furthermore, to circumvent sparse reward and sample imbalance problems over the microscopic road network, this article proposed a temporal-difference learning algorithm with prioritized gradient descent and adaptive exploration techniques. A simulator is built and trained with the Manhattan road network and New York City yellow taxi data to simulate the real-time vehicle dispatching environment. Both centralized and decentralized taxi dispatching policies are examined with the simulator. This case study shows that the proposed approach can further improve taxi drivers’ profits while reducing customers’ waiting times compared to several existing vehicle dispatching algorithms.
Neural Networks Enhanced Optimal Admittance Control of Robot–Environment Interaction Using Reinforcement Learning

In this paper, an adaptive admittance control scheme is developed for robots to interact with time-varying environments. Admittance control is adopted to achieve a compliant physical robot–environment interaction, and the uncertain environment with time-varying dynamics is defined as a linear system. A critic learning method is used to obtain the desired admittance parameters based on the cost function composed of interaction force and trajectory tracking without the knowledge of the environmental dynamics. To deal with dynamic uncertainties in the control system, a neural-network (NN)-based adaptive controller with a dynamic learning framework is developed to guarantee the trajectory tracking performance. Experiments are conducted and the results have verified the effectiveness of the proposed method.
Biological impact of mutually exclusive exon switching

Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch homologous exons and what are their biological impact? Here, we analyse the extent of sequence, structural and functional variability in MXEs and report the first large scale, structure-based analysis of the biological impact of MXE events from different genomes. MXE-specific residues tend to map to single domains, are highly enriched in surface exposed residues and cluster at or near protein functional sites. Thus, MXE events are likely to maintain the protein fold, but alter specificity and selectivity of protein function. This comprehensive resource of MXE events and their annotations is available at: http://gene3d.biochem. ucl.ac. uk/mxemod/. These findings highlight how small, but significant changes at critical positions on a protein surface are exploited in evolution to alter function.
Rationale and design of the precise percutaneous coronary intervention plan (P3) study: Prospective evaluation of a virtual computed tomography‐based percutaneous intervention planner

Fractional flow reserve (FFR) measured after percutaneous coronary intervention (PCI) has been identified as a surrogate marker for vessel related adverse events. FFR can be derived from standard coronary computed tomography angiography (CTA). Moreover, the FFR derived from coronary CTA (FFRCT) Planner is a tool that simulates PCI providing modeled FFRCT values after stenosis opening.
State Estimation for Probabilistic Boolean Networks via Outputs Observation

This article studies the state estimation for probabilistic Boolean networks via observing output sequences. Detectability describes the ability of an observer to uniquely estimate system states. By defining the probability of an observed output sequence, a new concept called detectability measure is proposed. The detectability measure is defined as the limit of the sum of probabilities of all detectable output sequences when the length of output sequences goes to infinity, and it can be regarded as a quantitative assessment of state estimation. A stochastic state estimator is designed by defining a corresponding nondeterministic stochastic finite automaton, which combines the information of state estimation and probability of output sequences. The proposed concept of detectability measure further performs the quantitative analysis on detectability. Furthermore, by defining a Markov chain, the calculation of detectability measure is converted to the calculation of the sum of probabilities of certain specific states in Markov chain. Finally, numerical examples are given to illustrate the obtained theoretical results.