Evaluating the performance of genomic selection on purebred population by incorporating crossbred data in pigs

Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it was limited by the purebred population.Compared to directly combining two uncorrelated purebred populations to extend the reference population size,it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.In this study,we simulated purebred offspring(PAS and PBS)and crossbred offspring(CAB)base on real genotype data of two base purebred populations(PA and PB),to evaluate the performance of genomic selection on purebred while incorporating crossbred information.The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship(REL)was better than the other methods(individuals closet or farthest to the purebred population,CP/FP)in term of the prediction accuracy.Furthermore,the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA,which was similar to combine PA and PAS.Moreover,the rank correlation between the multiple of the increased relationship(MIR)and reliability improvement was 0.60-0.70.But for individuals with low correlation(Cor(Pi,PA or B),the reliability improvement was significantly lower than other individuals.Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals.

Precise and accurate Ga isotope ratio measurements of geological samples by multi-collector inductively coupled plasma mass spectrometry

Gallium isotope is a potential geochemical tool for understanding planetary processes,environmental pollution,and ore deposit formation.The reported Ga isotope compositions(δ^(71)Ga NIST994 values)of some international geological standards,such as BCR-2 and BHVO-2 basalts,exhibit inconsistencies between diff erent laboratories.During mass spectrometry analysis,we found thatδ^(71)Ga NIST994 values of geological standards with or without the correction of the interference of^(138)Ba^(2+)(mass/charge ratio=69)on 69 Ga show signifi cant isotope off sets,and thus effi cient separation of Ba and correcting the interference of^(138)Ba^(2+)are both crucial to obtain accurateδ^(71)Ga values.By comparingδ^(71)Ga NIST994 values(relative to NIST SRM 994 Ga)of the same geostandards from diff erent laboratories,we suggest that the isotopic heterogeneity from NIST SRM 994 Ga is one of the key reasons for the inconsistencies inδ^(71)Ga NIST994 values of BCR-2 and BHVO-2.To facilitate inter-laboratory comparisons,we measured the Ga isotopic compositions of 11 geological reference materials(including Pb-Zn ore,bauxite,igneous rocks,and loess)and two Ga solution standards(NIST SRM 3119a and Alfa Aesar).Theδ^(71)Ga NIST994 andδ^(71)Ga IPGP values of these reference materials vary from 1.12‰to 2.63‰and−0.13‰to 1.38‰,respectively,and can be used to evaluate the precision and accuracy of Ga isotope data from diff erent laboratories.

Leveraging ROTI map derived from Indonesian GNSS receiver network for advancing study of Equatorial Plasma Bubble in Southeast/East Asia

This paper highlights the crucial role of Indonesia’s GNSS receiver network in advancing Equatorial Plasma Bubble(EPB)studies in Southeast and East Asia,as ionospheric irregularities within EPB can disrupt GNSS signals and degrade positioning accuracy.Managed by the Indonesian Geospatial Information Agency(BIG),the Indonesia Continuously Operating Reference Station(Ina-CORS)network comprises over 300 GNSS receivers spanning equatorial to southern low-latitude regions.Ina-CORS is uniquely situated to monitor EPB generation,zonal drift,and dissipation across Southeast Asia.We provide a practical tool for EPB research,by sharing two-dimensional rate of Total Electron Content(TEC)change index(ROTI)derived from this network.We generate ROTI maps with a 10-minute resolution,and samples from May 2024 are publicly available for further scientific research.Two preliminary findings from the ROTI maps of Ina-CORS are noteworthy.First,the Ina-CORS ROTI maps reveal that the irregularities within a broader EPB structure persist longer,increasing the potential for these irregularities to migrate farther eastward.Second,we demonstrate that combined ROTI maps from Ina-CORS and GNSS receivers in East Asia and Australia can be used to monitor the development of ionospheric irregularities in Southeast and East Asia.We have demonstrated the combined ROTI maps to capture the development of ionospheric irregularities in the Southeast/East Asian sector during the G5 Geomagnetic Storm on May 11,2024.We observed simultaneous ionospheric irregularities in Japan and Australia,respectively propagating northwestward and southwestward,before midnight,whereas Southeast Asia’s equatorial and low-latitude regions exhibited irregularities post-midnight.By sharing ROTI maps from Indonesia and integrating them with regional GNSS networks,researchers can conduct comprehensive EPB studies,enhancing the understanding of EPB behavior across Southeast and East Asia and contributing significantly to ionospheric research.

Accurate quantification of the algebraic,multiplicative algebraic,and simultaneous iterative reconstruction techniques in ionosphere rebuilding based on the TIEGCM assessment

The algebraic reconstruction technique(ART),multiplicative algebraic reconstruction technique(MART),and simultaneous iterative reconstruction technique(SIRT)are computational methodologies extensively utilized within the field of computerized ionospheric tomography(CIT)to facilitate three-dimensional reconstruction of the ionospheric morphology.However,reconstruction accuracy elicits recurrent disputes over its practical application,and people usually attribute this issue to incomplete and uneven coverage of the measurements.The Thermosphere Ionosphere Electrodynamics General Circulation Model(TIEGCM)offers a reasonable physics-based ionospheric background and is widely utilized in ionospheric research.We use the TIEGCM simulations as the targeted ionosphere because the current measurements are far from able to realistically reproduce the ionosphere in detail.Optimized designations of satellite measurements are conducted to investigate the limiting performance of CIT methods in ionospheric reconstruction.Similar to common practice,electron density distributions from outputs of the International Reference Ionosphere(IRI)model are used as the iterative initial value in CIT applications.The outcomes suggest that despite data coverage,iterative initial conditions also play an essential role in ionospheric reconstruction.In particular,in the longitudinal sectors where the iterative initial height of the F2-layer peak electron density(hmF2)differs substantially from the background densities,none of the three CIT methods can reproduce the exact background profile.When hmF2 is close but the ionospheric F2-layer peak density(NmF2)is different between the targeted background and initial conditions,the MART performs better than the ART and SIRT,as evidenced by the correlation coefficients of MART being above 0.97 and those of ART and SIRT being below 0.85.In summary,this investigation reveals the potential uncertainties in traditional CIT reconstruction,particularly when realistic hmF2 or NmF2 values differ substantially from the initial CIT conditions.

Bandgap Reference Design by Means of Multiple Point Curvature Compensation

A new method,namely multiple point curvature compensation （MPCC）,is proposed for the design of a bandgap reference,and its design principles, theoretical derivation, and one feasible circuitry implementation are presented. Being different from traditional techniques, this idea focuses on finding multiple temperatures in the whole range at which the first order derivatives of the output reference voltage equal zero. In this way, the curve of the output reference voltage is flattened and a better effect of curvature compensation is achieved. The circuitry is simulated in ST Microelectronics 0. 18μm CMOS technology, and the simulated result shows that the average temperature coefficient is only 1ppm/℃ in the range from - 40 to 125℃.

Screening of stable internal reference genes by quantitative real-time PCR in humpback grouper Cromileptes altivelis

Humpback grouper Cromileptes altivelis is one commercial fish with considerable economic value.To determine the expression stabilities of six commonly used internal reference genes in C.altivelis challenged by Vibrio harveyi and viral nervous necrosis virus(VNNV)through quantitative real-time PCR(qRT-PCR),the expression levels of selected genes in five immune organs stimulated with pathogenic infection were carefully evaluated using algorithms of geNorm,NormFinder,and BestKeeper.The results show that the expre ssion stabilities of the six candidate inte rnal reference genes were diffe re nt.Under no rmal physiological conditions,RPL13 were identified as the most stably expressed genes among five different immune organs(liver,spleen,kidney,intestine,and gill).After V.harveyi stimulation,RPL13,RPL13,EF1 A,RPL13,and EF1 A were identified by geNorm,NormFinder,and BestKeeper as the most stable genes in liver,spleen,kidney,intestine,and gill,respectively.Combining these three algorithms suggested that under stimulation of VNNV,RPL13,EF1 A,Actin,RPL13,and Actin were as the most stable genes in liver,spleen,kidney,intestine,and gill,respectively.These results suggest that specific experiment conditions and tissue types shall be considered when selecting the reference genes in qRT-PCR analysis.This study provided a solid foundation for future studies on gene expression of C.altivelis under different conditions.

Time-dependent Diffusion Coefficient and Conventional Diffusion Constant of Nanoparticles in Polymer Melts by Mode-coupling Theory

Time-dependent diffusion coefficient and conventional diffusion constant are calculated and analyzed to study diffusion of nanoparticles in polymer melts. A generalized Langevin equa- tion is adopted to describe the diffusion dynamics. Mode-coupling theory is employed to calculate the memory kernel of friction. For simplicity, only microscopic terms arising from binary collision and coupling to the solvent density fluctuation are included in the formalism. The equilibrium structural information functions of the polymer nanocomposites required by mode-coupling theory are calculated on the basis of polymer reference interaction site model with Percus-Yevick closure. The effect of nanoparticle size and that of the polymer size are clarified explicitly. The structural functions, the friction kernel, as well as the diffusion coefficient show a rich variety with varying nanoparticle radius and polymer chain length. We find that for small nanoparticles or short chain polymers, the characteristic short time non-Markov diffusion dynamics becomes more prominent, and the diffusion coefficient takes longer time to approach asymptotically the conventional diffusion constant. This constant due to the microscopic contributions will decrease with the increase of nanoparticle size, while increase with polymer size. Furthermore, our result of diffusion constant from mode- coupling theory is compared with the value predicted from the Stokes-Einstein relation. It shows that the microscopic contributions to the diffusion constant are dominant for small nanoparticles or long chain polymers. Inversely, when nanonparticle is big, or polymer chain is short, the hydrodynamic contribution might play a significant role.

Determination of Hf–Sr–Nd isotopic ratios by MC-ICP-MS using rapid acid digestion after flux-free fusion in geological materials

In this study, we established a rapid acid digestion for determining Hf-Sr-Nd isotopic ratios of geological samples by using MC-ICP-MS. Conditions of 1600 ℃ for 1 min and 1400 ℃ for 1 min were adopted for fusing intrusive rocks and extrusive rocks, respectively. The rapid acid digestion technique is superior in digestion time compared with high-pressure PTFE bomb method. The procedural blanks of the method were also lower than that flux fusion. Replicate analyses of international certified reference materials （CRMs） indicate that isotopic ratios of ^176Hf/^177Hf, ^87Sr/^86Sr and 143Nd/144Nd agree well with previously published data. The external reproducibility （2SD, n = 5） of ten CRMs are ±0.000030 for ^87Sr/^86Sr, ± 0.000030 for ^143Nd/^144Nd, and ±0.000018 for ^176Hf/^177Hf.

Characterization of the Engineering Flow in a Miniaturised Bioreactor by Computational Fluid Dynamics

Three approaches based on computational fluid dynamics(CFD) techniques have been assessed for their ability to describe the engineering flow environment in a miniaturized mechanically agitated bioreactor. The three approaches tested were the source-sink(SS), the multiple reference frames(MRF) and the sliding grids(SG). In all the cases, the predictions of the velocity components agree with reported experimental data. However, the analysis of the results of the turbulent intensities predicted by the three approaches indicates the MRF and the SG techniques under predicted turbulent intensities are comparable to both experimental measurements and the SS method. The predicted power number and pumping number based on the SS approach are closer to typical reported experimental values compared to those obtained from the MRF and SG methods.

Expression of Nitrilases in Brassica juncea var. tumida Tsen in Root Galls Caused by Plasmodiophora brassicae

Five commonly-used reference genes： ACT （actin）, UBE （ubiquitin-conjugating enzyme）, RPL2 （ribosomal protein L2）, BRP II （RNA polymerase II subunit）, and NADH （nicotinamide adenine dinucleotide） were examined using geNorm software as reference genes for RT-qPCR. Among the tested reference genes, ACT and UBE were the most stable in all samples. In parallel, expression analysis of nitrilases in Brassica juncea var. tumida, was performed to preliminarily investigate the molecular interactions between nitrilase and clubroot development at 10, 15, 20, 25, 30, and 40 d postinoculation （dpi） with a suspension of resting spores of Plasmodiophora brassicae. The results showed that different gene expressions of nitrilases were regulated during the initial periods of clubroot development. The expression level of BjNIT1 increased sharply from 20 to 40 dpi in infected roots while there were no remarkable changes in healthy roots. From 15 to 30 dpi, the expression levels of BjNIT2 and BjNIT4 in infected roots were lower than those in non-infected roots. Finally, BjNIT2 in treatment was down approximately to control at 40 dpi. Our results suggest that BjNIT1, which promoted overproductions of auxin, might be involved in P. brassicae infection of B. juncea.

FOUR WHEELS DRIVEN INDEPENDENTLY BY ONE PUMP DRIVING FOUR HYDRAULIC MOTORS

An improved Narendra model reference adaptive control (MRAC) scheme isproposed to research one variable displacement pump driving four hydraulic variable displacementmotors. This approach not only ensures the underdamped and unstable system be global uniformasymptotic stability, but also has good robustness in these aspects of modeling uncertainty,pressure fluctuation of constant pressure network, and disturbance from external load, which alsoupgrades the rapidity of system response so as to make controlled system with nicer dynamic quality.The scheme of one pump driving four motors can meet the demand on off-road mobility of engineeringvehicles and armored cars. A proof of stability about improved Narendra MRAC scheme is also given.

Selection of Reference Genes for Gene Expression Analysis in Nilaparvata lugens with Different Levels of Virulence on Rice by Quantitative Real-Time PCR

The brown planthopper Nilaparvata lugens Stal （Homoptera： Delphacidae） can cause hopperburn by feeding on rice and also can transmit the grassy stunt disease. Resistant rice varieties have been developed, but several N. lugens strains can recover their virulence to these resistant rice varieties. In the present study, reference genes with stable expression levels in N. lugens populations showed different levels of virulence to susceptible and resistant rice varieties. The expression of six candidate reference genes in N. lugens feeding on susceptible and resistant rice varieties was analyzed. These genes were evaluated for their potential use in the analysis of differential gene expression. Polymerase chain reaction data was generated from N. lugens, including two different treatments （resistant or susceptible rice） and three virulent N. lugens populations. Three software programs （BestKeeper, Normfinder and geNorm） were used to assess the candidate reference genes. Both geNorm and Normfinder identified the genes 18S, E-ACT, E-TUB and a-TUB as the most stable reference genes. BestKeeper identified ETIF1 as the optimal reference gene with the least overall variation, whereas 18S and a-TUB were the second and third most stably expressed genes, respectively. Therefore, we concluded that the genes 18S and a-TUB were the most suitable reference genes in N. lugens. These results will facilitate future transcript profiling studies on N. lugens populations that show variation in virulence levels on different rice varieties.

Assessment of internal controls for data normalization of gene expression after different bacterial stimulation by quantitative real-time PCR in golden pompano Trachinotus blochii

Trachinotus blochii is one of the important commercial fish species.In this study,we aim to confirm the reliability reference genes in T.blochii during different bacterial challenge through quantitative real-time PCR(qRT-PCR).The expression of the seven selected genes in four immune organs(i.e.,spleen,kidney,intestine,and gill)stimulated with Vibrio harveyi,Edwardsiella tarda,and Streptococcus agalactiae were determined by qRT-PCR.The PCR data was analyzed using the geNorm and NormFinder algorithms.The results showed the selection of the internal controls should be tissue specific when studying gene expression in response to bacterial stimulation.After 48 h of stimulation with V.harveyi,geNorm ranked EF1 A/Actin,18 S rRNA/B2M,UBCE/B2M,and 18 S rRNA/B2M,as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.After 48 h of stimulation with E.tarda,geNorm ranked 18 S rRNA/EF1 A,18 S rRNA/B2M,B2M/RPL13,and 18 S rRNA/EF1 A,as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.After 48 h of stimulation with S.agalactiae,18 S rRNA/EF1 A,18 S rRNA/B2 M,B2 M/Actin,and 18 S rRNA/B2M were ranked as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.Compared to the results analyzed by geNorm,reference genes received similar rankings when using NormFinder software.The results showed that the reference genes appeared to be not only tissue specific,but also specific to the infecting species of bacteria.If one gene is preferred when T.blochii were infected by bacteria,18 S rRNA,B2M,B2M,18 S rRNA may be used in spleen,kidney,intestine,and gill,respectively.

Parameter-independent error correction for potential measurements by reference electrode in lithium-ion batteries

The safety monitoring of lithium-ion batteries(LIBs) is of great significance for realizing all-climate and full-lifespan battery management. In-situ measurement of anode potential with implanted reference electrodes(REs) has proven to be effective to monitor and avoid the occurrence of severe side reactions like Li plating to ensure the safe and fast charging. However, the intrinsic measurement errors caused by local blocking effects, which also can be referred to as potential artefacts, are seldom taken into consideration in existing studies, yet they highly dominate the correctness of conclusions inferred from REs. In this study, aiming at exploring the physical origin of the measurement errors and ensure reliable potential monitoring, electrochemical and post-mortem tests are conducted using commercial pouch cells with implanted REs. Corresponding electrochemical model which describes the blocking effects, is established to validate the abnormal absence of lithium plating that predicted by measured anode potentials under various charging rates. Theoretical derivation is further presented to explain the error sources, which can be attributed to increased local liquid potential of the RE position. Most importantly, with the guidance of error analysis, a novel parameter-independent error correction method for RE measurements is proposed for the first time, which is proven to be adequate to estimate the real anode potentials and deduce the critical C-rate of Li plating with extra safety margin. After error correction, the resulting critical C-rates are all within the range of 0.55 ± 0.03 C, which is close to the C-rate of 0.6–0.7 C obtained from experiments. In addition, this error correction method can be performed conveniently with only some simple RE measurements of polarization voltages, totally independent of battery electrochemical and geometric parameters. This study provides highly practical error correction method for RE measurements in real LIBs, substantially facilitating the fast diagnosis and safety evaluation of Li plating during charging of LIBs.

Blind Image Quality Assessment by Pairwise Ranking Image Series

Image quality assessment(IQA)is constantly innovating,but there are still three types of stickers that have not been resolved:the“content sticker”-limitation of training set,the“annotation sticker”-subjective instability in opinion scores and the“distortion sticker”-disordered distortion settings.In this paper,a No-Reference Image Quality Assessment(NR IQA)approach is proposed to deal with the problems.For“content sticker”,we introduce the idea of pairwise comparison and generate a largescale ranking set to pre-train the network;For“annotation sticker”,the absolute noise-containing subjective scores are transformed into ranking comparison results,and we design an indirect unsupervised regression based on EigenValue Decomposition(EVD);For“distortion sticker”,we propose a perception-based distortion classification method,which makes the distortion types clear and refined.Experiments have proved that our NR IQA approach Experiments show that the algorithm performs well and has good generalization ability.Furthermore,the proposed perception based distortion classification method would be able to provide insights on how the visual related studies may be developed and to broaden our understanding of human visual system.

Future changes in rainfall, temperature and reference evapotranspiration in the central India by least square support vector machine

Climate change affects the environment and natural resources immensely. Rainfall, temperature and evapotranspiration are major parameters of climate affecting changes in the environment. Evapotrans- piration plays a key role in crop production and water balance of a region, one of the major parameters affected by climate change. The reference evapotranspiration or ETo is a calculated parameter used in this research. In the present study, changes in the future rainfall, minimum and maximum temperature, and ETo have been shown by downscaling the HadCM3 （Hadley Centre Coupled Model version 3） model data. The selected study area is located in a part of the Narmada river basin area in Madhya Pradesh in central India. The downscaled outputs of projected rainfall, ETo and temperatures have been shown for the 21st century with the HADCM3 data of A2 scenario by the Least Square Support Vector Machine （LS-SVM） model. The efficiency of the LS-SVM model was measured by different statistical methods. The selected predictors show considerable correlation with the rainfall and temperature and the application of this model has been done in a basin area which is an agriculture based region and is sensitive to the change of rainfall and temperature. Results showed an increase in the future rainfall, temperatures and ETo. The temperature increase is projected in the high rise of minimum temperature in winter time and the highest increase in maximum temperature is projected in the pre-monsoon season or from March to May. Highest increase is projected in the 2080s in 2081-2091 and 2091-2099 in maximum temperature and 2091-2099 in minimum temperature in all the stations. Winter maximum temperature has been observed to have increased in the future. High rainfall is also observed with higher ETo in some decades. Two peaks of the increase are observed in ETo in the April-May and in the October. Variation in these parameters due to climate change might have an impact on the future water resource of the study area, which is mainly an agricultural based region, and will help in proper planning and management.

Validation of reference genes for gene expression studies in the dinoflagellate Akashiwo sanguinea by quantitative real-time RT-PCR

The accurate measurement of gene expression via quantitative real-time reverse transcription PCR（q RT-PCR）heavily relies on the choice of valid reference gene（s） for data normalization. Resting cyst is the dormant stage in the life cycle of dinoflagellate, which plays crucial roles in HAB-forming dinoflagellate ecology. However, only limited investigations have been conducted on the reference gene selection in dinoflagellates. Gap remained in our knowledge about appropriate HKGs for normalizing gene expression in different life stages, which laid obstacles for the application of q RT-PCR to the HAB-forming group. In this study, six candidate reference genes,18 S ribosomal RNA（18S）, glyceraldehyde-3-phosphate dehydrogenase（GAPDH）, α-tubulin（TUA）, β-tubulin（TUB）, actin（ACT） and cytochrome oxidase subunit 1（COX1）, were evaluated for their expression stability with q RT-PCR and three statistical algorithms（Ge Norm, Norm Finder, and Best Keeper） for the cosmopolitan, harmful algal bloom-forming dinoflagellate Akashiwo sanguinea. Expression patterns were observed across 18 biological samples, including cells at resting stages（resting cysts）, different growth stages, in darkness, exposed to abscisic acid（ABA） and exposed to temperature stress. The results indicated that TUA, 18 S and GAPDH were relatively stable across all tested scenarios. While the best-recommended reference genes differed across experimental groups, the pairs of ACT and TUA, 18 S and GAPDH were the most reliable for cells at different growth stages and darkness treatment. The combination of TUA and TUB was the best choice for normalization in resting cysts and in ABA treatment, respectively. The pair of ACT and COX1 was suitable for temperature treatments. This study was the first to investigate the stable internal reference genes in dinoflagellates at different stages of life cycle,particularly in resting cysts. Our results provided useful information for selection of reference genes in dinoflagellates regarding quantification of gene expression at different experimental scenarios, which will facilitate more accurate and widespread use of q RT-PCR in gene analysis of dinoflagellates and help to design primers targeting orthologous genes in other algal species.

A Confession Caused by Laughter─Albert Camus and His Novel＂The Fall＂

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A Review of＂Some Basic Principles of Teacher Training＂and＂British and American Methodology＂in NEW ORIENTTIONS IN THE TEACHING OF ENGLISH By Peter Strevens

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Genome Size of Alexandrium catenella and Gracilariopsis lemaneiformis Estimated by Flow Cytometry

Flow cytometry(FCM) technique has been widely applied to estimating the genome size of various higher plants. However, there is few report about its application in algae. In this study, an optimized procedure of FCM was exploited to estimate the genome size of two eukaryotic algae. For analyzing Alexandrium catenella, an important red tide species, the whole cell instead of isolated nucleus was studied, and chicken erythrocytes were used as an internal reference. The genome size of A. catenella was estimated to be 56.48 ± 4.14 Gb(1C), approximately nineteen times larger than that of human genome. For analyzing Gracilariopsis lemaneiformis, an important economical red alga, the purified nucleus was employed, and Arabidopsis thaliana and Chondrus crispus were used as internal references, respectively. The genome size of Gp. lemaneiformis was 97.35 ± 2.58 Mb(1C) and 112.73 ± 14.00 Mb(1C), respectively, depending on the different internal references. The results of this research will promote the related studies on the genomics and evolution of these two species.