Miracle-dz/UniFAR-FTUs huggingface dataset:
Protective and Detoxifying Enzyme Activity and ABCG Subfamily Gene Expression in Sogatella furcifera Under Insecticide Stress

Sogatella furcifera, an important migratory pest of rice, has substantial detrimental effects on rice production. To clarify the mechanism whereby S. furcifera responds to insecticide stress, we measured the activity of its protective [superoxide dismutase (SOD); peroxidase (POD); catalase (CAT)] and detoxifying [carboxylesterase (CarE); glutathione S-transferase (GST); mixed-function oxidase (MFO)] enzymes and the expression levels of its ATP-binding cassette subfamily G (ABCG) transporter genes in response to sublethal concentrations (LC10 and LC25) of the insecticides thiamethoxam, buprofezin, and abamectin. On the bases of the transcriptome data and the ABCG genes of Laodelphax striatellus, we obtained 14 full-length ABCG sequences for S. furcifera. RT-qPCR results showed that 13, 12, and 9 sfABCG genes were upregulated in the presence of thiamethoxam, buprofezin, and abamectin, respectively, at LC10. Moreover, 13 and 7 sfABCG genes were upregulated following treatment with thiamethoxam and abamectin, respectively, at LC25. Enzyme activity assays showed that although thiamethoxam, buprofezin, and abamectin induced GST, CarE, CAT, POD, and SOD activity, they did so at different concentrations and exposure times. The activity of MFO was generally inhibited with prolonged exposure to the three insecticides, with the inhibitory effect being most significant at 72 h. These results indicate that S. furcifera differs in its response to different types or concentrations of insecticides. Taken together, our results lay the foundations for gaining a deeper understanding of the mechanisms underlying the adaptation of S. furcifera to different types of insecticides, which would be of considerable significance for the development of effective pest management strategies.
Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations

Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n = 411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n = 9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n = 36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r2 ≥ 0.2 extended up to ~50 kb in crossbred and 170 kb in purebred populations, while average r2 values ≥0.3 were respectively observed in the ~10 and 60 kb in the crossbred and purebred populations. The largest phase correlation (RP, C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes.
IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections

Interferon-induced transmembrane proteins (IFITMs) are a family of small proteins that localize in the plasma and endolysosomal membranes. IFITMs not only inhibit viral entry into host cells by interrupting the membrane fusion between viral envelope and cellular membranes, but also reduce the production of infectious virions or infectivity of progeny virions. Not surprisingly, some viruses can evade the restriction of IFITMs and even hijack the antiviral proteins to facilitate their infectious entry into host cells or promote the assembly of virions, presumably by modulating membrane fusion. Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Here, we review the function and potential impact of genetic variation for IFITM restriction of viral infections. Continuing research efforts are required to decipher the molecular mechanism underlying the complicated interaction among IFITMs and viruses in an effort to determine their pathobiological roles in the context of viral infections in vivo.
Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation

YabT is a serine/threonine kinase of the Hanks family from Bacillus subtilis, which lacks the canonical extracellular signal receptor domain but is anchored to the membrane through a C-terminal transmembrane helix. A previous study demonstrated that a basic juxtamembrane region corresponds to a DNA-binding motif essential for the activation of YabT trans-autophosphorylation. YabT is expressed during spore development and localizes to the asymmetric septum where it specifically phosphorylates essential proteins involved in genome maintenance, such as RecA, SsbA, and YabA. YabT has also been shown to phosphorylate proteins involved in protein synthesis, such as AbrB and Ef-Tu, suggesting a possible regulatory role in the progressive metabolic quiescence of the forespore. Finally, cross phosphorylations with other protein kinases implicate YabT in the regulation of numerous other cellular processes. Using an artificial protein scaffold as crystallization helper, we determined the first crystal structure of this DNA-dependent bacterial protein kinase. This allowed us to trap the active conformation of the kinase domain of YabT. Using NMR, we showed that the basic juxtamembrane region of YabT is disordered in the absence of DNA in solution, just like it is in the crystal, and that it is stabilized upon DNA binding. In comparison with its closest structural homolog, the mycobacterial kinase PknB allowed us to discuss the dimerization mode of YabT. Together with phosphorylation assays and DNA-binding experiments, this structural analysis helped us to gain new insights into the regulatory activation mechanism of YabT.
Modélisation probabiliste d'essais en laboratoire par processus gaussien avec peu de spécimens répliqués

RESUME Les essais experimentaux en laboratoire, tels que les essais sur des specimens de beton, demandent de grandes ressources financieres. En effet, fabriquer un specimen de beton peut couter quelques milliers de dollars. Ainsi, il est frequent que seuls quelques specimens repliques soient soumis a l’essai etudie. Le jeu de donnees experimentales est constitue des observations mesurees qui sont fonction des valeurs de la donnee d’entree soit de la covariable. Ce jeu de donnees constitue a partir de seulement quelques specimens testes est alors assez pauvre en informations. ----------ABSTRACT Laboratory experiments can be very expensive and so require an important budget, for example manufacturing concrete specimens can cost thousands of dollars. That is why, it is common to only test few replicated specimens. Because of a weak set of data, it is difficult to draw a reliable model from it, only the behaviour tendency can be caught and qualitative conclusions can be made. This project aims at building a probabilistic method able to model laboratory experiments with a set of data including only few replicated specimens.
Polyspectra-based, blind, MMSE, fractionally-spaced equalization of a cyclostationary signal

Two weaknesses of polyspectra-based blind equalization are addressed. The first weakness involves a zero-forcing (ZF) characteristic, where intersymbol interference is eliminated with disregard for associated mean squared error (MSE). It is shown that a minimum-MSE (MMSE) constraint can be added for signals operating in colored Gaussian noise, with only a small increase in computational complexity and with performance enhancement under certain scenarios. The second weakness involves the constraint that the signal be stationary, which fails to exploit the cyclostationary features of most communication signals (W. A. Gardner). In particular, it is shown that polyspectra-based techniques can be used with a fractionally-spaced equalizer, with attendant performance boosts in timing insensitivity (S. H. Qureshi, 1985) and damaged-spectrum restoration (W. A. Gardner, 1991). The technique decomposes the signal into stationary streams, computing the individual and joint statistics of the partitions, and then solves the optimal Wiener equation. <<ETX>>
On the split structure of lifted groups

Let wp: tildeX -> X be a regular covering projection of connected graphs with the group of covering transformations CT_wp being abelian. Assuming that a group of automorphisms G CT_wp -> tildeG -> G -> id splits is analyzed in detail in terms of a Cayley voltage assignment that reconstructs the projection up to equivalence. In the above combinatorial setting the extension is given only implicitly: neither tildeG nor the action G -> Aut CT_wp nor a 2-cocycle GxG -> CT_wp, are given. Explicitly constructing the cover tildeX together with CT_wp and tildeG as permutation groups on tildeX is time and space consuming whenever CT_wp is large; thus, using the implemented algorithms (for instance, HasComplement in Magma) is far from optimal. Instead, we show that the minimal required information about the action and the 2-cocycle can be effectively decoded directly from voltages (without explicitly constructing the cover and the lifted group); one could then use the standard method by reducing the problem to solving a linear system of equations over the integers. However, along these lines we here take a slightly different approach which even does not require any knowledge of cohomology. Time and space complexity are formally analyzed whenever CT_wp is elementary abelian.
Pyramid vector quantization applied to a video coding scheme for contribution quality

A novel effective video coding scheme for contribution quality is presented. Starting from the CMTT/2 proposal, a modified video coding scheme obtained by introducing vector quantization instead of scalar quantization is presented. In particular, pyramid vector quantization (PVQ), able to exploit the Laplacian distribution of discrete cosine transform (DCT) coefficients, has been chosen as the VQ method. Two DCT coefficient coding strategies have been tested, based on stripe and field base, both using an efficient design of vectors to be quantized. Simulations show that the proposed video coding scheme, without introducing considerable computational effort and working at 22 Mbit/s, gives the same contribution quality as the CMTT/2 proposal at 45 Mbit/s. <<ETX>>
Connected and degraded text recognition using planar hidden Markov models

An algorithm for connected text recognition using enhanced planar hidden Markov models (PHMMs) is presented. The algorithm automatically segments text into characters (even if they are highly blurred and touching) as an integral part of the recognition process, thus jointly optimizing segmentation and recognition. Performance is enhanced by the use of state length models, transition probabilities among characters (bigrams), and grammars. Experiments are presented using: (1) a simulated database of over 24000 highly degraded images of city names and (2) a database of 6000 images rejected by a high-performance commercial OCR (optical character recognition) machine with 99.5% accuracy. Measured performance on the first database is 99.65% for the most degraded images when a grammar is used, and 98.76% in the second database. Traditional OCR algorithms would fail drastically on these images. <<ETX>>
Improving upper bounds for the distinguishing index

The distinguishing index of a graph G , denoted by D ʹ( G ) , is the least number of colours in an edge colouring of G not preserved by any non-trivial automorphism. We characterize all connected graphs G with D ʹ( G ) ≥ Δ ( G ) . We show that D ʹ( G ) ≤ 2 if G is a traceable graph of order at least seven, and D ʹ( G ) ≤ 3 if G is either claw-free or 3 -connected and planar. We also investigate the Nordhaus-Gaddum type relation: 2 ≤ D ʹ( G ) + D ʹ( ‾ G ) ≤ max{Δ ( G ), Δ ( ‾ G )} + 2 and we confirm it for some classes of graphs.
Special purpose correlation functions for improved signal detection and parameter estimation

A compilation of several correlation functions which were developed by the author and have been used for several years in signal analysis applications is given. The affine invariant pseudometric is a correlation function normalized to be independent of power, DC bias, and phase rotation. It was developed to track radar video sync pulses. It has recently been successfully used to track glottal pulses in voiced speech. The cross-power spectrum represents a significant improvement over standard power-spectral methods for recovering weak stationary tones in noise. The harmonic rejecting correlation function is a variant of the Wigner transform which resolves fundamentals from harmonic and subharmonic features produced by periodic waveforms. Each of these algorithms has been tested and used on a variety of data. Most importantly, for each of the methods described here, closed form solutions are derived, which enable easy implementations. <<ETX>>
A 37-GHz-Input Divide-by-36 Injection-Locked Frequency Divider with 1.6-GHz Lock Range

This paper presents a divide-by-36 injection-locked frequency divider (ILFD). It locks onto a 37-GHz input over a locking range of about 1.6 GHz (4.3%) and outputs a frequency of approximately 1GHz, which is sufficiently low for further division by a programmable divider. The high division ratio is realized by time-gating the superharmonic input signal and injecting it into a 9-stage ring VCO at 9 feeding points. Nine gating signals are generated by the ring VCO itself by logic operation such that the input signal is injected only during the correct time slice for each of the feeding points. The ILFD was fabricated using a 55-nm deeply depleted channel (DDC) CMOS process, occupies an area of 0.020 mm2, and consumes a power of 9.1 mW.
A Compact High Efficiency and High Power Front-end Module for GSM/EDGE/TD-SCDMA/TD-LTE Applications in 0.13um CMOS

This work presents a multimode multiband transmitter front-end module (TXM) fully integrated on a new 4-layer laminate substrate process supporting GSM/EDGE/TD-SCDMA/TD-LTE. In the TXM, a new compact power amplifier (PA) matching network including transformer and harmonic filter is proposed on this process with low insertion loss. An adaptive bias circuit is also proposed to enhance the PA linearity. The TXM including the 0.13um CMOS PA, SP16T antenna switch and all passive components is fully integrated in a flip-chip LGA package. Compared with other works, the measurement results of this work show 30dBm high linear power with 19% high power-added efficiency(PAE) in 915MHz EDGE mode. It also shows high linear power of 27dBm and 24dBm in TD-SCDMA mode and TD-LTE mode, respectively. The proposed TXM meets the class E2 power requirement with enough output power margin and high efficiency.
A 28mn 320Kb TCAM Macro with Sub-0.8ns Search Time and 3.5+x Improvement in Delay-Area-Energy Product using Split-Controlled Single-Load 14T Cell

This work proposes a Split-Controlled Single-Load (SCSL) 14T TCAM cell to achieve (1) compact cell area, (2) reduced search delays and energy, (3) less leakage current. A 320Kb 14T-TCAM macro was fabricated using a 28nm CMOS process and modified foundry compact-area 6T cell. The resulting macro lowered search delays to just 710ps and gained a 3.5+x improvement in the figure-of-merit (delay-area-energy product), compared to conventional 16T TCAMs.
An adaptive reconstruction method involving discontinuities

A novel deterministic reconstruction method preserving discontinuities is presented. This method is based on a Markov random field image model, coupled with a line-process. The reconstruction method uses a deterministic and adaptive relaxation algorithm. This algorithm is presented for single photon emission computed tomography (SPECT) reconstruction, but can also be applied to a large class of inverse problems in image processing. The experimental results are very promising. The proposed method is robust to noise and yields good results. The reconstructed images are composed of smooth areas, bordered by sharp edges. <<ETX>>
More about wavelet maxima representations

Results regarding reconstruction and modifications of multiscale (wavelet) maxima and zero-crossings representations are presented. The work is based on a general signal description, called an inherently bounded adaptive quasi-linear representation (AQLR), motivated by two important examples: the wavelet maxima representation and the wavelet zero-crossings representation. The convergence of two novel reconstruction algorithms is guaranteed for all inherently bounded AQLRs. Modifications in the basic multiscale maxima representation which make it possible to trade-off between amount of required information and the reconstruction quality are described. <<ETX>>
Geometric point-circle pentagonal geometries from Moore graphs

We construct isometric point-circle configurations on surfaces from uniform maps. This gives one geometric realisation in terms of points and circles of the Desargues configuration in the real projective plane, and three distinct geometric realisations of the pentagonal geometry with seven points on each line and seven lines through each point on three distinct dianalytic surfaces of genus 57. We also give a geometric realisation of the latter pentagonal geometry in terms of points and hyperspheres in 24 dimensional Euclidean space. From these, we also obtain geometric realisations in terms of points and circles (or hyperspheres) of pentagonal geometries with k circles (hyperspheres) through each point and k-1 points on each circle (hypersphere).
Isospectral genus two graphs are isomorphic

By a graph we mean a finite connected multigraph without bridges. The genus of a graph is the dimension of its homology group. Two graphs are isospectral is they share the same Laplacian spectrum. We prove that two genus two graphs are isospectral if and only if they are isomorphic. Also, we present two bridgeless genus three graphs that are not isomorphic. The paper is motivated by the following open problem posed by Peter Buser: are isospectral Riemann surfaces of genus two isometric?
Application of orthogonal-search method to Volterra modeling of nonlinear systems

The orthogonal-search technique is utilized to reduce the number of filter coefficients required to describe Volterra kernels up to third order. To demonstrate the efficacy of the approach, the orthogonal-search technique is applied to two experimental data sets exhibiting quadratic and cubic nonlinearities, respectively. The results show that this method can reduce the required number of filter coefficients considerably, while still providing a good model of the nonlinear physical system. <<ETX>>
A 12.4TOPS/W, 20% Less Gate Count Bidirectional Phase Domain MAC Circuit for DNN Inference Applications

A small gate count 8 bit bidirectional phase domain MAC (PMAC) circuit is proposed for DNN inference applications targeting IoT edge. PMAC consumes significantly smaller power than standard fully digital MACs, owing to its efficient analog accumulation nature based on Gated-Ring-Oscillator (GRO). Compared with the previous first PoC of PMAC, the bidirectional architecture proposed in this paper achieves 20% less gate count, which is comparable with fully digital MACs, and relaxes system design constraints by eliminating phase error originating in leakage current. Asynchronous readout technique and 2-step DTC for the better system throughput and compact implementation, respectively, are presented for the first time. The PMAC achieves peak efficiency of 12.4 TOPS/W in 28 nm CMOS.
Color filter selection for color correction in the presence of noise

The effect of noise on the number of effective channels (color filters) used to record a color image is investigated. Transmittances of color filters are calculated which minimize the mean square error that occurs when estimating, from the recorded data, the colors in the image under a collection of viewing illuminants. Since the results indicate that a significant improvement in color correction accuracy is achieved by using four channels, there is good reason to consider using four-tuples for the representation of colorimetric information. <<ETX>>
Texture coding using a pyramid decomposition

The weighted multiresolution process model (WiMP) has been shown to combine the scale and time frequency localization properties of the wavelet representation with the self-affine characteristics of signals generated by iterated function systems (IFSs). It maintains the properties of the IFS model and resolves the instability of the inverse problem by introducing more parameters. Based on the conjecture that while IFSs are deterministic models they can synthesize natural looking textures, examples of modeling and reconstruction of real textures using WiMPs are presented. It is observed that, in the case of natural textures, the performance of the model is sensitive to the space and frequency localization of the wavelet decomposition. The deterministic model for self-affine signals considered here could be added to multiresolution techniques that lack textural information. Its localization in space makes it flexible for fitting local textures. <<ETX>>
Testing whether the lifted group splits

Let a group of automorphisms lift along a regular covering projection of connected graphs given combinatorially by means of voltages. The data that determine the lifted group and its action are then conveniently encoded in terms of voltages as well. Along these lines, an algorithm for testing whether the lifted group is a split extension of the group of covering transformations has recently been proposed in the case when the group of covering transformations is solvable. It consists of decomposing the covering into a series of coverings with elementary abelian groups of covering transformations, and inductively solving the problem at every elementary abelian step. Although the explicit construction of the lifted group is not needed, it still involves time and space consuming constructions of certain subgroups in the lifted group at every step except at the final one. In this paper, an improved version that completely avoids such constructions is presented. From voltage distribution we first compute the weak action and the factor set that determine the lifted group, and we then carry out the test by extracting the necessary information only from the corresponding weak actions and factor sets at every step. An experimental comparison is made against the previous version.
A 3.9μW, 81.3dB SNDR, DC-coupled, Time-based Neural Recording IC with Degeneration R-DAC for Bidirectional Neural Interface in 180nm CMOS

This paper presents a 5-bit VCO-based neural recording IC, which directly quantizes the input signal and achieves a large dynamic range (DR) to process the small-amplitude neural signal in the presence of the large-amplitude stimulation artifact (SA). A feedback-controlled source degeneration is applied to the input transconductor circuit (Gm,in) by using a resistor DAC (R-DAC). It mitigates the circuit nonlinearity, resulting in a large signal-to-noise-and-distortion ratio (SNDR) and a high input impedance (Zin). The implemented neural recording IC achieves 813dB SNDR over 200Hz signal bandwidth and 200mVPP maximum allowable input range while consuming 3. 9μW per channel.