Miracle-dz/UniFAR-FTUs huggingface dataset:
Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers

True genetically encoded monomeric fluorescent timers (tFTs) change their fluorescent color as a result of the complete transition of the blue form into the red form over time. Tandem FTs (tdFTs) change their color as a consequence of the fast and slow independent maturation of two forms with different colors. However, tFTs are limited to derivatives of the mCherry and mRuby red fluorescent proteins and have low brightness and photostability. The number of tdFTs is also limited, and there are no blue-to-red or green-to-far-red tdFTs. tFTs and tdFTs have not previously been directly compared. Here, we engineered novel blue-to-red tFTs, called TagFT and mTagFT, which were derived from the TagRFP protein. The main spectral and timing characteristics of the TagFT and mTagFT timers were determined in vitro. The brightnesses and photoconversions of the TagFT and mTagFT tFTs were characterized in live mammalian cells. The engineered split version of the TagFT timer matured in mammalian cells at 37 °C and allowed the detection of interactions between two proteins. The TagFT timer under the control of the minimal arc promoter, successfully visualized immediate-early gene induction in neuronal cultures. We also developed and optimized green-to-far-red and blue-to-red tdFTs, named mNeptusFT and mTsFT, which were based on mNeptune-sfGFP and mTagBFP2-mScarlet fusion proteins, respectively. We developed the FucciFT2 system based on the TagFT-hCdt1-100/mNeptusFT2-hGeminin combination, which could visualize the transitions between the G1 and S/G2/M phases of the cell cycle with better resolution than the conventional Fucci system because of the fluorescent color changes of the timers over time in different phases of the cell cycle. Finally, we determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis.
Portable multichannel multiwavelength near-infrared diffusive light imager

We have developed a near infrared optical tomography system features fast optical switching, three-wavelength excitations, and avalanche photodiode (APD) detectors with a high dynamic range. Pigtailed laser diodes at 660, 780, and 830 nm are used as light sources and their outputs are distributed sequentially to one of nine source fibers. The crosstalk between source channels is around 65 dB, equivalent to 130 dB in opto-electrical signals. 10 Silicon APD’s detect diffusive photon density waves simultaneously. The dynamic range of an APD is several orders higher than that of a photomultiplier tube (PMT), which eliminates the need of multi-step system gain control. However, the internal gain of the APD we are using is about 3 orders lower than an ordinary PMT. Efforts have been made to suppress the feed through interferences from the transmission part to the reception part so as to reduce the errors in amplitude and phase measurements.
Enabling Energy-Efficient In-Memory Computing With Robust Assist-Based Reconfigurable Sense Amplifier in SRAM Array

With the increasing gap between processing speed and memory bandwidth necessity for in/near-memory computing has emerged, to ensure high-performance, energy-efficient computing for data-intensive applications at the edge. This work proposes a feasible SRAM compute cache with a sense amplifier (SA) based approach to perform in-/near memory Boolean computations with a novel reconfigurable assist sense amplifier (RASA). The RASA exploits assist transistors to achieve NAND, NOR and XNOR operations without affecting the transparency of normal read leading to fast and reliable sensing with only one SA. This effectively eliminates the need for two SAs in comparison to state-of-the-art solutions. The proposed work improves memory density and reduces cost-per-bit by leveraging the SA-based approach because existing solutions lead to significant area overhead/cell which reflects overhead multiply by the number of cells/column. The RASA provides flexibility to accommodate more cells per column at the architecture level. Extensive Monte-Carlo analysis is performed to verify the feasibility of the proposed circuit in commercial 65nm UMC technology under iso-SA area and iso-yield conditions. Simulations indicate a 34.34%, 84.87%, 81.21%, 75.46% improvement in energy, and a 71.30%, 43.36%, 32.49%, 17.44% improvement in throughput leading to a reduction of 60.97%, 91.37%, 87.22%, 79.62% in energy-delay product with respect to CLSA (Dong et al., 2018), CSRAM (Chen et al., 2021), RRCSA (Rajput et al., 2022) and the ADSA (Agrawal et al., 2018) respectively. An improvement in the area of SA by 36.512% is achieved with respect to RRCSA.
Computation of system balancing transformations and other applications of simultaneous diagonalization algorithms

An algorithm is presented in this paper for computing state-space balancing transformations directly from a state-space realization. The algorithm requires no "squaring up" or unnecessary matrix products. Various algorithmic aspects are discussed in detail. A key feature of the algorithm is the determination of a contragredient transformation through computing the singular value decomposition of a certain product of matrices without explicitly forming the product. Other contragredient transformation applications are also described. It is further shown that a similar approach may be taken, involving the generalized singular value decomposition, to the classical simultaneous diagonalization problem. These SVD-based simultaneous diagonalization algorithms provide a computational alternative to existing methods for solving certain classes of symmetric positive definite generalized eigenvalue problems.
The theorem analysis on optical flow estimation from three frames of image sequences

The method presented, based on three frames of an image sequence, avoids using any supplementary constrained requirement such as smoothness requirement. According to the inertia theorem in kinematics, the velocity of an object point is considered constant during the three consecutive images, so that the acceleration of the moving object point is set to zero. A series of simple operations lead to a second-order equation about the component U of displacement vector. A discrimination function is established to select one accurate solution from the two equations' solutions. Another component, V, can be derived from the original line-constrained equation. <<ETX>>
Thymoquinone ameliorates acrylamide-induced reproductive toxicity in female rats: An experimental study

Abstract Background Acrylamide (AA) is a carcinogenic compound that causes severe reproductive impairments and represents a high environmental risk factor. Thymoquinone (TQ) has a unique antioxidant activity and has been widely used as a protective agent against various types of toxicity. Objective To evaluate the protective effects of TQ against AA-induced reproductive toxicity in female rats. Materials and Methods In this experimental study, 40 female albino rats (120-150 gr, 8-10 wk) were sorted into 4 groups, (n = 10/each), vehicle group (received a daily oral administration of 0.5 ml saline [9%]); AA group (received a daily oral administration with freshly prepared AA, 20 mg/kg body weight) for 21 days which is less than the lethal dose LD 50 of AA in rats (20 mg/kg body weight); AA+TQ group (received a daily oral administration of TQ, 10 mg/kg body weight) after AA intoxication for 21 days, and TQ group (received a daily oral administration of TQ only, 10 mg/kg body weight) for 21 consecutive days. Reproductive hormones, carcinogenic biomarkers, and oxidative stress markers were measured. The histological assessment showed the protective effect of TQ against AA-induced ovarian injury. Network pharmacology analysis and molecular docking approach were carried out to determine the binding affinity of TQ with cyclooxygenase 2. Results TQ administration significantly enhanced the functional capacity of the ovary at hormones, oxidative biomarkers, and tumor markers at a significant level of p < 0.001. Besides, TQ protects the ovary of AA-treated rats from the severe degeneration effect. Conclusion TQ showed a promising protective effect against AA-induced reproductive toxicity in female rats.
Identification of the Putative Binding Site of a Benzimidazole Opioid (Etazene) and Its Metabolites at µ-Opioid Receptor: A Human Liver Microsomal Assay and Systematic Computational Study

The synthetic benzimidazole opioid etazene (which has a 70-times higher analgesic activity than morphine), a recreational drug, has gained popularity as a novel psychoactive substance (NPS) on the illegal/darknet market; however, no experimental information is available at the molecular level on the binding mechanism and putative binding site of etazene and its metabolites at the µ-opioid receptor (MOR). In the present study, we investigated the metabolism of etazene in human liver microsomes using ultra-high-performance liquid chromatography–mass spectrometry (UHPLC–MS). We also explored the possibilities of MOR activation by etazene and its metabolites by studying their binding mechanisms and interaction profiles at an active-state MOR model via molecular docking, binding free energy calculations, and all-atom molecular dynamics (MD) simulations. The putative metabolites of etazene were also predicted using the ADMET Predictor 10.1. The molecular docking studies and free energy calculations showed that etazene and its metabolites (M1, M2, and M5–M7) exhibited strong predicted binding affinity at MOR and showed overlapped binding orientation with MOR-bound agonist BU72, which was co-crystallized in the MOR X-ray crystal structure (PDB ID: 5C1M). MD also confirmed the stability of the MOR–etazene and MOR–M6 complexes. These results suggest that etazene and its metabolites may act as strong MOR agonists, highlighting the necessity of experimental validation. The insights from this study, such as key interactions between etazene and its metabolites and the MOR, will allow authorities to predict potential analogs and clarify the target–protein interactions associated with this illicit substance, granting advanced or rapid reactions to confiscating or banning potential emerging drugs.
The colored branch theorem and its applications in circuit theory

The colored branch theorem (Minty 1960 [1]) is a result in graph theory, which essentially says that the existence (resp., nonexistence) of a certain loop immediately implies the nonexistence (resp., existence) of a certain cutset. Its relevance and use in circuit theory, however, has only recently been recognized. Since it is expected that many more applications in circuit theory will follow, the theorem is interpreted and proved in a network setting. Many graph-theoretic corollaries are derived, which may facilitate later use. It is illustrated that many results in circuit theory can he simplified or given a simpler proof using this theorem and its corollaries.
Lack of nuclear differentiation suggests reproductive connectivity between the ‘southern feeding group’ and the larger population of eastern North Pacific gray whales, despite previous detection of mitochondrial differences

During winter, eastern North Pacific gray whales migrate south to calving grounds in the lagoons of Baja California, and in spring they migrate north to their summer feeding grounds in the Chukchi and Beaufort Seas. Although the majority of the population makes this migration, a small subset of the population known as the ‘southern feeding group’ ends their northward migration early, spending summers feeding in waters ranging from northern California to southern Alaska. Previous analyses based on photo-ID and mtDNA data indicate that this seasonal substructuring results from maternally-directed site fidelity to different feeding grounds, and that this site fidelity and feeding ground preference is passed from mothers to their offspring. It is currently assumed, but not known, that the individuals of the southern feeding group mate with the rest of the population, and therefore that the eastern North Pacific gray whale represents one interbreeding population. Testing this assumption and understanding how these whales are related to the rest of the population, is key to making appropriate management decisions, which are particularly relevant given the recent increase in potential removals, or threats in the area such as the proposed resumption of aboriginal whaling, and increased oil pipeline development and subsequent vessel traffic. This paper analyses 15 nuclear microsatellite loci in 59 individuals from the southern feeding group and 40 individuals from the calving lagoons (representative of the larger population) to test the hypothesis that the eastern North Pacific gray whale represents one interbreeding population. No indication of population substructuring was found based on these nuclear loci, suggesting that all sampled whales do indeed represent one interbreeding population. Combined, these data from mitochondrial and nuclear markers therefore suggest one interbreeding population that is seasonally subdivided based on maternally-directed site fidelity to different feeding areas.
ISO LMF 24613-6: A Revised Syntax Semantics Module for the Lexical Markup Framework

The Lexical Markup Framework (LMF) is a meta-model for representing data in monolingual and multilingual lexical databases with a view to its use in computer applications. The "new LMF" replaces the old LMF standard, ISO 24613:2008, and is being published as a multi-part standard. This short paper introduces one of these new parts, ISO 24613-6, namely the Syntax and Semantics (SynSem) module. The SynSem module allows for the description of syntactic and semantic properties of lexemes, as well as the complex interactions between them. While the new standard remains faithful to (and backwards compatible with) the syntax and semantics coverage of the previous model, the new standard clarifies and simplifies it in a few places, which will be illustrated.
A new global model with two electron groups for weakly ionized argon discharges at low pressure

A new global model is developed for weakly ionized argon discharges at low pressure with a non-Maxwellian electron energy distribution. This model adopts the ‘two-electron group approximation’, as done in reference (Vriens L 1973 J. Appl. Phys. 44 3980; Ligthart F A S and Keijser R A J 1980 J. Appl. Phys. 51 5295; Kudryavtsev A A and Tsendin L D 2002 Tech. Phys. Lett. 28 841), but the effective temperatures for both groups of electrons, the energy boundary between them in energy space and the total volume-averaged electron density are all obtained in a self-consistent manner. By treating low- and high-energy electrons as two different species and involving particle and energy balance equations for both of them, the model-predicted electron distributions agree well with the measured ones under a wide range of discharge conditions. A detailed comparison between the results from the model presented in this work and those from the previous models is also made, along with the discussion of the reasons that cause the differences.
Atomistic Study for the Tantalum and Tantalum–Tungsten Alloy Threshold Displacement Energy under Local Strain

The threshold displacement energy (TDE) is an important measure of the extent of a material’s radiation damage. In this study, we investigate the influence of hydrostatic strains on the TDE of pure tantalum (Ta) and Ta–tungsten (W) alloy with a W content ranging from 5% to 30% in 5% intervals. Ta–W alloy is commonly used in high-temperature nuclear applications. We found that the TDE decreased under tensile strain and increased under compressive strain. When Ta was alloyed with 20 at% W, the TDE increased by approximately 15 eV compared to pure Ta. The directional-strained TDE (Ed,i) appears to be more influenced by complex 〈i j k〉 directions rather than soft directions, and this effect is more prominent in the alloyed structure than in the pure one. Our results suggest that radiation defect formation is enhanced by tensile strain and suppressed by compressive strain, in addition to the effects of alloying.
Dynamical hierarchical self‐organization of harmonic and motivic musical categories

We introduce a generic model of emergence of musical categories during the listening process. The model is based on a preprocessing and a categorization module. Preprocessing results in a perceptually plausible representation of music events extracted from symbolic input. The categorization module lets a taxonomy of musical entities emerge according to a cognitively plausible online learning paradigm. We show the advantages of using a conceptual clustering method in the musical domain. The system extracts multilevel hierarchies and can be tuned to clustering at various resolutions. The potential of the model is exemplified by exposing it to two different datasets resulting in music harmonic and motivic categorization consistent with music theory.
C 59 o NMR shift anomalies and spin dynamics in the normal state of superconducting CeCoIn 5 : Verification of two-dimensional antiferromagnetic spin fluctuations

We have measured the Knight shifts $(K)$ and nuclear relaxation times $({T}_{1})$ for $^{59}\text{C}\text{o}$ in ${\text{CeCoIn}}_{5}$ under external fields along $a$ and $c$ axes with the goal of establishing the anisotropy of antiferromagnetic (AFM) spin fluctuations (SF). In our approach, we revisit the problem of interpreting anomalies in the relationship between Knight shift ${K}_{a,c}$ and static susceptibility ${\ensuremath{\chi}}_{a,c}$: assuming a single component susceptibility implies a temperature-dependent hyperfine coupling ${A}_{a,c}(T)$. Once adopted, a known discrepancy between the behaviors of ${T}_{1}^{\ensuremath{-}1}$ for $^{59}\text{C}\text{o}$ and $^{115}\text{I}\text{n}(1)$ sites is eliminated to within experimental uncertainties and the variation with temperature is analyzed within the framework of two-dimensional AFM SF in proximity to a quantum-critical point. Moreover, the ratio $[{T}_{1a}/{T}_{1c}]$ indicates easy-plane anisotropy for $Tl{T}^{\ensuremath{\ast}}\ensuremath{\sim}40\text{ }\text{K}$, for the heavy-fermion state.
Lyman-Alpha Emission in Star-forming Galaxies: Low-Redshift Counterparts of Primeval Galaxies?

UV plus optical spectra of three galaxies, Mrk 496, Mrk 357, Tol 1924-416, obtained by matching the size of the optical aperture with that of IUE are presented. From the Hα/Hβ ratios, values of E(B-V), extinction due to dust, are estimated for the two Markarian galaxies which are higher than those derived in previous works. The new values of E(B-V) have been used to deredden the Lyα fluxes, although this technique can be considered an approximation of the detailed extinction process, since it is unlikely that the dust is homogeneously distributed within a galaxy
Profiling the miRNA from Exosomes of Non-Pigmented Ciliary Epithelium-Derived Identifies Key Gene Targets Relevant to Primary Open-Angle Glaucoma

Oxidative stress (OS) on tissues is a major pathological insult leading to elevated intraocular pressure (IOP) and primary open-angle glaucoma (POAG). Aqueous humor (AH) produced by the non-pigmentary ciliary epithelium (NPCE) drains out via the trabecular meshwork (TM) outflow pathway in the anterior chamber. The exosomes are major constituents of AH, and exosomes can modulate the signaling events, as well as the responses of their target TM tissue. Despite the presence of molecular mechanisms to negate OS, oxidative damage directly, as well as indirectly, influences TM health, AH drainage, and IOP. We proposed that the expression of microRNA (miRNAs) carried by exosomes in the AH can be affected by OS, and this can modulate the pathways in target cells. To assess this, we subjected NPCE to acute and chronic OS (A-OS and C-OS), enriched miRNAs, performed miRNA microarray chip analyses, and miRNA-based gene targeting pathway prediction analysis. We found that various miRNA families, including miR27, miR199, miR23, miR130b, and miR200, changed significantly. Based on pathway prediction analysis, we found that these miRNAs can regulate the genes including Nrf2, Keap1, GSK3B, and serine/threonine-protein phosphatase2A (PP2A). We propose that OS on the NPCE exosomal miRNA cargo can modulate the functionality of the TM tissue.
Income and Child Maltreatment: Evidence from a Discontinuity in Tax Benefits

Poverty is one of the leading predictors of child maltreatment, yet the causal relationship is not wellunderstood. In this paper I provide new evidence of the effects of income on child protection system (CPS) referrals, investigations and foster care placements. I exploit a discontinuity in child-related tax benefits around a January 1 birthdate, which results in otherwise-similar families receiving considerably different refunds during the first year of a child’s life. I use 20 years of linked administrative data from California to determine the effects of this additional income on CPS involvement. A one-time $1,000 transfer to low-income households decreases the number of referrals to CPS in the first 3 years of a child’s life by approximately 3%. These effects persist throughout the system, decreasing investigations (3%) and days spent in foster care (8%). Effects also persist throughout childhood, reducing CPS involvement through at least age 8. Heterogeneity analyses by allegation and reporter category as well as by child race and gender suggest that these effects capture true reductions in maltreatment, as opposed to changes in reporting behavior. These findings suggest that providing low-income families with additional resources during the first year of a child’s life are a fruitful strategy for reducing child maltreatment. ∗University of California, San Diego, Department of Economics. Contact e-mail: krittenh@ucsd.edu. I am grateful for helpful comments from Prashant Bharadwaj, Alyssa Brown, Julie Cullen, Gordon Dahl, Natalia Emanuel, Rebecca Fraenkel, Katherine Meckel, Emily Putnam-Hornstein, and David Simon. I wish to acknowledge the Children’s Data Network for housing and maintaining the data used in this project. Data infrastructure support was provided to the Children’s Data Network by First 5 LA, The Conrad N. Hilton Foundation, and the Heising-Simons Foundation. All opinions, conclusions and errors are my own.
QTL Mapping for Wheat Seed Dormancy in a Yangmai16/Zhongmai895 Double Haploid Population

Pre-harvest sprouting (PHS) of wheat reduces grain yield and quality, and it is strongly affected by seed dormancy. Therefore, identification of quantitative trait loci (QTL) for seed dormancy is essential for PHS resistance breeding. A doubled haploid (DH) population, consisting of 174 lines from the cross between Yangmai16 (YM16) and Zhongmai895 (ZM895) was used to detect QTLs for seed dormancy and grain color. For seed dormancy, a total of seven QTLs were detected on chromosomes 2A, 3A, 3D, 4D, 5B and 5D over four environments, among which Qdor.hzau-3A, Qdor.hzau-3D.1 and Qdor.hzau-3D.2 were stably detected in more than two environments. For grain color, only two QTLs, Qgc.hzau-3A and Qgc.hzau-3D were detected on chromosomes 3A and 3D, which physically overlapped with Qdor.hzau-3A and Qdor.hzau-3D.1, respectively. Qdor.hzau-3D.2 has never been reported elsewhere and is probably a novel locus with allelic effect of seed dormancy contributed by weakly dormant parent ZM895, and a KASP marker was developed and validated in a wheat natural population. This study provides new information on the genetic dissection of seed dormancy, which may aid in further improvement for marker-assisted wheat breeding for PHS resistance.