Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

A Study to Observe Pulse Pressure Variation after Induction with Propofol for General Anesthesia

Background and Aims: Pulse pressure variation (PPV) is a reliable and predictive dynamic parameter presently being utilized for fluid responsiveness. In the operating room, fluid administration based on PPV monitoring helps the physician in deciding whether to volume resuscitate or use interventions in patients undergoing surgery. Propofol is an intravenous induction agent which lowers blood pressure. There are multiple causes such as depression in cardiac output, and peripheral vasodilatation for hypotension. We undertook this study to observe the utility of PPV as a guide to fluid therapy after propofol induction. Primary outcome of our study was to monitor PPV as a marker of fluid responsiveness for the hypotension caused by propofol induction. Secondary outcome included the correlation of PPV with other hemodynamic parameters like heart rate (HR), systolic blood pressure (SBP), and diastolic blood pressure (DBP);after induction with propofol at regular interval of time. Methods: A total number of 90 patients were recruited. Either of the radial artery was then cannulated under local anaesthesia with 20G VygonLeadercath arterial cannula and invasive monitoring transduced. A baseline recording of heart rate (HR), systolic blood pressure (SBP), diastolic blood pressure (DBP) and PPV was then recorded. Patients were then induced with predetermined doses of propofol (2 mg/kg) and recordings of HR, SBP, DBP, and PPV were taken at 5, 10 and 15 minutes. Results: Intraoperatively, PPV was significantly higher at 5 minutes and significantly lower at 15 minutes after induction. It was observed that there were no statistically significant correlations between PPV and SBP or DBP. PPV was strongly and directly associated with HR. Conclusion: We were able to establish that PPV predicts fluid responsiveness in hypotension caused by propofol induction;and can be used to administer fluid therapy in managing such hypotension. However, PPV was not directly correlated with hypotension subsequent to propofol administration.

The Variation of Plankton Community Structure in Artificial Reef Area and Adjacent Waters in Haizhou Bay

Plankton are an important component of marine protected areas(MPAs),and its communities would require much smaller interpatch distances to ensure connection among MPAs.According to the survey from MPAs dominated by artificial reefs and adjacent waters(estuary area(EA),aquaculture area(AA),artificial reef area(ARA),natural area(NA)and comprehensive effect area(CEA))in Haizhou Bay in spring and autumn,we analyzed phyto-zooplankton composition,abundance and biomass,and correlation with hydrologic variables to gain information about the forces that structure the plankton.The results showed that the dominant zooplankton were copepods(spring,98.9%;autumn,94.2%),while the phytoplankton were mainly composed of Bacillariophyta(spring,61.8%;autumn,95.6%).The RDA results showed that temperature,salinity and depth highly associated with the distribution and composition of plankton species among the habitats than other factors in spring;temperature,Chla and DO had the strongest influence in autumn.The zooplankton in the ARA and AA ecosystems basically contained the same species as those in other habitats,and each habitat also exhibited a relatively unique combination of plankton species.The structures of the EA zooplankton in spring and the EA phytoplankton in both seasons were much different than other habitats,which may have been caused by factors such as currents and tides.We concluded that there exists similarity of the plankton community between artificial reef area and adjacent waters,whereas the EAs may be relatively independent systems.Therefore,these interaction between plankton community should be considered when designing MPA networks,and ocean circulations should be considered more than the environmental factors.

Seasonal Variation of Hearing Sensitivity in the Red-eared Slider(Trachemys scripta elegans)

Seasonal variation of hearing sensitivity has been observed in many vertebrate groups with obvious vocal behaviors.Circulating hormones,conspecific calling signals,and temperature are potential factors that drive these plasticity patterns.Turtles have a hearing range that appears to be limited to under 1.5 kHz and are often thought to be non-vocal;thus,they are commonly neglected in vocal communication research.In this study,we aimed to determine whether the auditory phenotype exhibits seasonal variation in sensitivity and to analyze the potential factors driving such variation patterns in turtles.We measured hearing sensitivity and sex hormone levels in female(estradiol)and male(testosterone and dihydrotestosterone)Red-eared sliders(Trachemys scripta elegans)during spring and winter.The results showed that auditory brainstem response(ABR)thresholds were significantly lower in spring than in winter at a frequency range of 0.5-0.9 kHz.The hearing-sensitivity bandwidth was wider,and the ABR latency was significantly shorter in spring than in winter.No significant differences were found in estradiol,testosterone,and dihydrotestosterone levels in T.scripta elegans between spring and winter.This study is the first to reveal the seasonal variation of peripheral hearing sensitivity in turtles,a special animal group with limited hearing range and less vocalization.Temperature variations may be used to explain these seasonal effects,but further research is required to confirm our findings.

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic traits.Constructing a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.Results To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples.By constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose genomes.Furthermore,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition traits.For instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length.Notably,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild counterparts.Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.Conclusion This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits,thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese.Moreover,assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome,establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

A novel diurnal and seasonal variation analysis of BTEX in Bengaluru urban area

In the urban atmosphere of Bengaluru, various volatile organic compounds(VOCs), particularly Benzene,Toluene, Ethylbenzene, and Xylene(BTEX), have shown an increasing trend in concentration. The present research was conducted during summer and monsoon seasons, focusing on Kadubeesanahalli, a high-traffic area within the Bengaluru Metropolitan City. Hourly sample data was collected using a BTEX analyzer(Model GC955-600) and subsequently transformed into daily, monthly, and seasonal values. The study revealed distinct patterns in benzene concentrations. Benzene levels were lowest during the early morning hours, specifically from 1:00 a.m.to 7:00 a.m.. Concentrations then increased from 7:00 a.m. to 9:00 a.m. and again from 4:00 p.m. to 11:00 p.m.,corresponding to the morning and evening peak traffic hours. However, between 10:00 a.m. and 4:00 p.m., the concentration decreased due to reduced traffic levels. These diurnal variations in benzene concentration are influenced by meteorological parameters. Comparing the two seasons, higher concentrations of Benzene, EthylBenzene, and MP-xylene were observed during the summer season. This increase is attributed to the elevated temperatures during summer, which promote the vaporization of BTEX compounds. Conversely, lower BTEX concentrations were recorded during the monsoon season due to the wet deposition process. The observed positive correlation(r > 0.5) among BTEX parameters strongly suggests a common source, most likely originating from vehicular emissions.

Annual variation of adult survival of a south-temperate House Wren population in Argentina

Identifying factors affecting the survival of individuals is essential for understanding the evolution of life-history traits and population dynamics.Despite numerous studies on this subject in north-temperate environments,there is a lack of equivalent studies at similar latitudes in the south.Here,we used a 14-year dataset of capture,banding,and resighting to estimate the annual variation in the apparent adult survival probability of a south-temperate population of House Wrens(Troglodytes aedon bonariae).We evaluated temporal variation in sur-vival and the effect of environmental(climatic)and demographic variables(adult abundance,total number of fledglings produced during each breeding season)on survival estimators.We found that the probability of adult survival decreased as the abundance of breeding adults increased.This density-dependent effect could be related to the resident lifestyle of southern House Wrens,which could determine an intense competition for territories and resources that ultimately would affect their survival.

STRONGLY CONVERGENT INERTIAL FORWARD-BACKWARD-FORWARD ALGORITHM WITHOUT ON-LINE RULE FOR VARIATIONAL INEQUALITIES

This paper studies a strongly convergent inertial forward-backward-forward algorithm for the variational inequality problem in Hilbert spaces.In our convergence analysis,we do not assume the on-line rule of the inertial parameters and the iterates,which have been assumed by several authors whenever a strongly convergent algorithm with an inertial extrapolation step is proposed for a variational inequality problem.Consequently,our proof arguments are different from what is obtainable in the relevant literature.Finally,we give numerical tests to confirm the theoretical analysis and show that our proposed algorithm is superior to related ones in the literature.

Variational Learned Talking-Head Semantic Coded Transmission System

Video transmission requires considerable bandwidth,and current widely employed schemes prove inadequate when confronted with scenes featuring prominently.Motivated by the strides in talkinghead generative technology,the paper introduces a semantic transmission system tailored for talking-head videos.The system captures semantic information from talking-head video and faithfully reconstructs source video at the receiver,only one-shot reference frame and compact semantic features are required for the entire transmission.Specifically,we analyze video semantics in the pixel domain frame-by-frame and jointly process multi-frame semantic information to seamlessly incorporate spatial and temporal information.Variational modeling is utilized to evaluate the diversity of importance among group semantics,thereby guiding bandwidth resource allocation for semantics to enhance system efficiency.The whole endto-end system is modeled as an optimization problem and equivalent to acquiring optimal rate-distortion performance.We evaluate our system on both reference frame and video transmission,experimental results demonstrate that our system can improve the efficiency and robustness of communications.Compared to the classical approaches,our system can save over 90%of bandwidth when user perception is close.

The study of lithographic variation in resistive random access memory

Reducing the process variation is a significant concern for resistive random access memory(RRAM).Due to its ultrahigh integration density,RRAM arrays are prone to lithographic variation during the lithography process,introducing electrical variation among different RRAM devices.In this work,an optical physical verification methodology for the RRAM array is developed,and the effects of different layout parameters on important electrical characteristics are systematically investigated.The results indicate that the RRAM devices can be categorized into three clusters according to their locations and lithography environments.The read resistance is more sensitive to the locations in the array(~30%)than SET/RESET voltage(<10%).The increase in the RRAM device length and the application of the optical proximity correction technique can help to reduce the variation to less than 10%,whereas it reduces RRAM read resistance by 4×,resulting in a higher power and area consumption.As such,we provide design guidelines to minimize the electrical variation of RRAM arrays due to the lithography process.

An efficient parallel algorithm of variational nodal method for heterogeneous neutron transport problems

The heterogeneous variational nodal method(HVNM)has emerged as a potential approach for solving high-fidelity neutron transport problems.However,achieving accurate results with HVNM in large-scale problems using high-fidelity models has been challenging due to the prohibitive computational costs.This paper presents an efficient parallel algorithm tailored for HVNM based on the Message Passing Interface standard.The algorithm evenly distributes the response matrix sets among processors during the matrix formation process,thus enabling independent construction without communication.Once the formation tasks are completed,a collective operation merges and shares the matrix sets among the processors.For the solution process,the problem domain is decomposed into subdomains assigned to specific processors,and the red-black Gauss-Seidel iteration is employed within each subdomain to solve the response matrix equation.Point-to-point communication is conducted between adjacent subdomains to exchange data along the boundaries.The accuracy and efficiency of the parallel algorithm are verified using the KAIST and JRR-3 test cases.Numerical results obtained with multiple processors agree well with those obtained from Monte Carlo calculations.The parallelization of HVNM results in eigenvalue errors of 31 pcm/-90 pcm and fission rate RMS errors of 1.22%/0.66%,respectively,for the 3D KAIST problem and the 3D JRR-3 problem.In addition,the parallel algorithm significantly reduces computation time,with an efficiency of 68.51% using 36 processors in the KAIST problem and 77.14% using 144 processors in the JRR-3 problem.

Analysis of the Spatiotemporal Variation Characteristics and Driving Factors of Land Vegetation GPP in a Certain Region of Asia

Gross primary productivity (GPP) of vegetation is a critical indicator of ecosystem growth and carbon sequestration. The spatiotemporal variation characteristics of land vegetation GPP trends in a specific region of Asia from 2001 to 2020 were analyzed by Sen and MK trend analysis methods in this study .Moreover , a GPP change attribution model was established to explore the driving influences of factors such as Leaf Area Index (LAI), Land Surface Temperature (LST), Vapor Pressure Deficit (VPD), Soil Moisture, Solar Radiation and Wind Speed on GPP. The results indicate that summer GPP values are significantly higher than those in other months, accounting for 60.8% of the annual total GPP;spring and autumn contribute 18.91% and 13.04%, respectively. In winter, due to vegetation being nearly dormant, the contribution is minimal at 7.19%. Spatially, GPP shows a decreasing trend from southeast to northwest. LAI primarily drives the spatial and seasonal variations of regional GPP, while VPD, surface temperature, solar radiation, and soil moisture have varying impacts on GPP across different dimensions. Additionally, wind speed exhibits a minor contribution to GPP across different dimensions.

Seasonal variation of mesoscale eddy intensity in the global ocean

Mesoscale eddies are a prominent oceanic phenomenon that plays an important role in oceanic mass transport and energy conversion.Characterizing by rotational speed,the eddy intensity is one of the most fundamental properties of an eddy.However,the seasonal spatiotemporal variation in eddy intensity has not been examined from a global ocean perspective.In this study,we unveil the seasonal spatiotemporal characteristics of eddy intensity in the global ocean by using the latest satellite-altimetry-derived eddy trajectory data set.The results suggest that the eddy intensity has a distinct seasonal variation,reaching a peak in spring while attaining a minimum in autumn in the Northern Hemisphere and the opposite in the Southern Hemisphere.The seasonal variation of eddy intensity is more intense in the tropical-subtropical transition zones within latitudinal bands between 15°and 30°in the western Pacific Ocean,the northwestern Atlantic Ocean,and the eastern Indian Ocean because baroclinic instability in these areas changes sharply.Further analysis found that the seasonal variation of baroclinic instability precedes the eddy intensity by a phase of 2–3 months due to the initial perturbations needing time to grow into mesoscale eddies.

Variational Neural Inference Enhanced Text Semantic Communication System

Recently,deep learning-based semantic communication has garnered widespread attention,with numerous systems designed for transmitting diverse data sources,including text,image,and speech,etc.While efforts have been directed toward improving system performance,many studies have concentrated on enhancing the structure of the encoder and decoder.However,this often overlooks the resulting increase in model complexity,imposing additional storage and computational burdens on smart devices.Furthermore,existing work tends to prioritize explicit semantics,neglecting the potential of implicit semantics.This paper aims to easily and effectively enhance the receiver's decoding capability without modifying the encoder and decoder structures.We propose a novel semantic communication system with variational neural inference for text transmission.Specifically,we introduce a simple but effective variational neural inferer at the receiver to infer the latent semantic information within the received text.This information is then utilized to assist in the decoding process.The simulation results show a significant enhancement in system performance and improved robustness.

Intraspecific floral colour variation in three Pedicularis species

Flower constancy describes the phenomenon that pollinators tend to successively visit flowers of a single species during foraging,reducing reproductive interference in natural communities.The extent of flower constancy is largely determined by the floral traits of co-flowering species.Both higher inter-specific and lower intraspecific differences of floral traits should contribute to a higher level of flower constancy.However,previous studies mainly focused on interspecific difference,and the intraspecific variation(consistency)of floral traits received much less attention.We hypothesise that selection may favour lower intraspecific floral trait variation in communities composed of multiple co-flowering congeners.We investigated the floral colour variation of three focal Pedicularis species that share pollinators in 19communities composed of either single or multiple Pedicularis species.Colour was quantified using image-based colour analysis as perceived by pollinators.We found that most of the intrapopulation floral colour variation was below the colour discrimination threshold of bumblebees,implying strongly constrained by the visual selection by pollinators.Contrary to the hypothesis,there is no significant difference in intraspecific floral colour variation between different community contexts.It may be due to the relatively large interspecific floral colour differences of most co-flowering species.The influence of community context on intraspecific variation may be reflected in floral traits other than colours.

Dynamic thermo-mechanical responses of road-soft ground system under vehicle load and daily temperature variation

A complete road-soft ground model is established in this paper to study the dynamic responses caused by vehicle loads and/or daily temperature variation.A dynamic thermo-elastic model is applied to capturing the behavior of the rigid pavement,the base course,and the subgrade,while the soft ground is characterized using a dynamic thermo-poroelastic model.Solutions to the road-soft ground system are derived in the Laplace-Hankel transform domain.The time domain solutions are obtained using an integration approach.The temperature,thermal stress,pore water pressure,and displacement responses caused by the vehicle load and the daily temperature variation are presented.Results show that obvious temperature change mainly exists within 0.3 m of the road when subjected to the daily temperature variation,whereas the stress responses can still be found in deeper places because of the thermal swelling/shrinkage deformation within the upper road structures.Moreover,it is important to consider the coupling effects of the vehicle load and the daily temperature variation when calculating the dynamic responses inside the road-soft ground system.

Natural variation of GmFNSII-2 contributes to drought resistance by modulating enzyme activity in soybean

As an essential crop that provides vegetable oil and protein,soybean(Glycine max(L.)Merr.)is widely planted all over the world.However,the scarcity of water resources worldwide has seriously impacted on the quality and yield of soybean.To address this,exploring excellent genes for improving drought resistance in soybean is crucial.In this study,we identified natural variations of GmFNSII-2(flavone synthase II)significantly affect the drought resistance of soybeans.Through sequence analysis of GmFNSII-2 in 632 cultivated and 44 wild soybeans nine haplotypes were identified.The full-length allele GmFNSII-2^(C),but not the truncated allele GmFNSII-2^(A) possessing a nonsense nucleotide variation,increased enzyme activity.Further research found that GmDREB3,known to increase soybean drought resistance,bound to the promoter region of GmFNSII-2^(C).GmDREB3 positively regulated the expression of GmFNSII-2^(C),increased flavone synthase abundance and improved the drought resistance.Furthermore,a singlebase mutation in the GmFNSII-2^(C) promoter generated an additional drought response element(CCCCT),which had stronger interaction strength with GmDREB3 and increased its transcriptional activity under drought conditions.The frequency of drought-resistant soybean varieties with Hap 1(Pro:GmFNSII-2^(C))has increased,suggesting that this haplotype may be selected during soybean breeding.In summary,GmFNSII-2^(C) could be used for molecular breeding of drought-tolerant soybean.

Variational Reconstruction and Simulation Experiments of Sea Surface Wind Field for Ocean Data Buoy

The sea surface wind field is an important physical parameter in oceanography and meteorology.With the continuous refinement of numerical weather prediction,air-sea interface materials,energy exchange,and other studies,three-dimensional(3D)wind field distribution at local locations on the sea surface must be measured accurately.The current in-situ observation of sea surface wind parameters is mainly achieved through the installation of wind sensors on ocean data buoys.However,the results obtained from this single-point measurement method cannot reflect wind field distribution in a vertical direction above the sea surface.Thus,the present paper proposes a theoretical framework for the optimal inversion of the 3D wind field structure variation in the area where the buoy is located.The variation analysis method is first used to reconstruct the wind field distribution at different heights of the buoy,after which theoretical analysis verification and numerical simulation experiments are conducted.The results indicate that the use of variational methods to reconstruct 3D wind fields is significantly effective in eliminating disturbance errors in observations,which also verifies the correctness of the theoretical analysis of this method.The findings of this article can provide a reference for the layout optimization design of wind measuring instruments in buoy observation systems and also provide theoretical guidance for the design of new observation buoys in the future.

The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.