Genome-wide investigation to assess copy number variants in the Italian local chicken population

Background Copy number variants(CNV)hold significant functional and evolutionary importance.Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock.High-density chips have enabled the detection of CNV with increased resolution,leading to the identification of even small CNV.This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome.Results Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV.The majority of CNV in the investigated breeds were of types 0 and 1,and the minimum length of CNV was significantly larger than that reported in previous studies.Interestingly,a high proportion of the length of chromosome 16 was covered by copy number variation regions(CNVR),with the major histocompatibility complex being the likely cause.Among the genes identified within CNVR,only those present in at least five animals across breeds(n=95)were discussed to reduce the focus on redundant CNV.Some of these genes have been associated to functional traits in chickens.Notably,several CNVR on different chromosomes harbor genes related to muscle development,tissue-specific biological processes,heat stress resistance,and immune response.Quantitative trait loci(QTL)were also analyzed to investigate potential overlapping with the identified CNVR:54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size,carcass characteristics,egg production,egg components,fat deposition,and feed intake.Conclusions The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

Present situation and prospect of immunotherapy for unresectable locally advanced esophageal cancer during peri-radiotherapy

Four major studies(Checkmate577,Keynote-590,Checkmate649 and Attraction-4)of locally advanced esophageal cancer published in 2020 have established the importance of immunotherapy,represented by anti-programmed death protein(PD)-1 in postoperative adjuvant treatment and advanced first-line treatment of locally advanced or advanced esophageal cancer and esophagogastric junction cancer,from the aspects of proof of concept,long-term survival,overall survival rate and progression-free survival.For unresectable or inoperable nonmetastatic esophageal cancer,concurrent radiotherapy and chemotherapy is the standard treatment recommended by various guidelines.Because its curative effect is still not ideal,it is necessary to explore radical radiotherapy and chemotherapy in the future,and it is considered to be promising to combine them with immunotherapeutic drugs such as anti-PD-1.This paper mainly discusses how to combine radical concurrent radiotherapy and chemotherapy with immunotherapy for unresectable local advanced esophageal cancer.

Deep brain implantable microelectrode arrays for detection and functional localization of the subthalamic nucleus in rats with Parkinson’s disease

The subthalamic nucleus(STN)is considered the best target for deep brain stimulation treatments of Parkinson’s disease(PD).It is difficult to localize the STN due to its small size and deep location.Multichannel microelectrode arrays(MEAs)can rapidly and precisely locate the STN,which is important for precise stimulation.In this paper,16-channel MEAs modified with multiwalled carbon nanotube/poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate)(MWCNT/PEDOT:PSS)nanocomposites were designed and fabricated,and the accurate and rapid identification of the STN in PD rats was performed using detection sites distributed at different brain depths.These results showed that nuclei in 6-hydroxydopamine hydrobromide(6-OHDA)-lesioned brains discharged more intensely than those in unlesioned brains.In addition,the MEA simultaneously acquired neural signals from both the STN and the upper or lower boundary nuclei of the STN.Moreover,higher values of spike firing rate,spike amplitude,local field potential(LFP)power,and beta oscillations were detected in the STN of the 6-OHDA-lesioned brain,and may therefore be biomarkers of STN localization.Compared with the STNs of unlesioned brains,the power spectral density of spikes and LFPs synchronously decreased in the delta band and increased in the beta band of 6-OHDA-lesioned brains.This may be a cause of sleep and motor disorders associated with PD.Overall,this work describes a new cellular-level localization and detection method and provides a tool for future studies of deep brain nuclei.

Assessment of earthquake location uncertainties for the design of local seismic networks

The ability to estimate earthquake source locations,along with the appraisal of relevant uncertainties,is paramount in monitoring both natural and human-induced micro-seismicity.For this purpose,a monitoring network must be designed to minimize the location errors introduced by geometrically unbalanced networks.In this study,we first review different sources of errors relevant to the localization of seismic events,how they propagate through localization algorithms,and their impact on outcomes.We then propose a quantitative method,based on a Monte Carlo approach,to estimate the uncertainty in earthquake locations that is suited to the design,optimization,and assessment of the performance of a local seismic monitoring network.To illustrate the performance of the proposed approach,we analyzed the distribution of the localization uncertainties and their related dispersion for a highly dense grid of theoretical hypocenters in both the horizontal and vertical directions using an actual monitoring network layout.The results expand,quantitatively,the qualitative indications derived from purely geometrical parameters(azimuthal gap(AG))and classical detectability maps.The proposed method enables the systematic design,optimization,and evaluation of local seismic monitoring networks,enhancing monitoring accuracy in areas proximal to hydrocarbon production,geothermal fields,underground natural gas storage,and other subsurface activities.This approach aids in the accurate estimation of earthquake source locations and their associated uncertainties,which are crucial for assessing and mitigating seismic risks,thereby enabling the implementation of proactive measures to minimize potential hazards.From an operational perspective,reliably estimating location accuracy is crucial for evaluating the position of seismogenic sources and assessing possible links between well activities and the onset of seismicity.

Impact of different interaction behavior on epidemic spreading in time-dependent social networks

We investigate the impact of pairwise and group interactions on the spread of epidemics through an activity-driven model based on time-dependent networks.The effects of pairwise/group interaction proportion and pairwise/group interaction intensity are explored by extensive simulation and theoretical analysis.It is demonstrated that altering the group interaction proportion can either hinder or enhance the spread of epidemics,depending on the relative social intensity of group and pairwise interactions.As the group interaction proportion decreases,the impact of reducing group social intensity diminishes.The ratio of group and pairwise social intensity can affect the effect of group interaction proportion on the scale of infection.A weak heterogeneous activity distribution can raise the epidemic threshold,and reduce the scale of infection.These results benefit the design of epidemic control strategy.

SNR and RSSI Based an Optimized Machine Learning Based Indoor Localization Approach:Multistory Round Building Scenario over LoRa Network

In situations when the precise position of a machine is unknown,localization becomes crucial.This research focuses on improving the position prediction accuracy over long-range(LoRa)network using an optimized machine learning-based technique.In order to increase the prediction accuracy of the reference point position on the data collected using the fingerprinting method over LoRa technology,this study proposed an optimized machine learning(ML)based algorithm.Received signal strength indicator(RSSI)data from the sensors at different positions was first gathered via an experiment through the LoRa network in a multistory round layout building.The noise factor is also taken into account,and the signal-to-noise ratio(SNR)value is recorded for every RSSI measurement.This study concludes the examination of reference point accuracy with the modified KNN method(MKNN).MKNN was created to more precisely anticipate the position of the reference point.The findings showed that MKNN outperformed other algorithms in terms of accuracy and complexity.

Survey of Indoor Localization Based on Deep Learning

This study comprehensively examines the current state of deep learning (DL) usage in indoor positioning.It emphasizes the significance and efficiency of convolutional neural networks (CNNs) and recurrent neuralnetworks (RNNs). Unlike prior studies focused on single sensor modalities like Wi-Fi or Bluetooth, this researchexplores the integration of multiple sensor modalities (e.g.,Wi-Fi, Bluetooth, Ultra-Wideband, ZigBee) to expandindoor localization methods, particularly in obstructed environments. It addresses the challenge of precise objectlocalization, introducing a novel hybrid DL approach using received signal information (RSI), Received SignalStrength (RSS), and Channel State Information (CSI) data to enhance accuracy and stability. Moreover, thestudy introduces a device-free indoor localization algorithm, offering a significant advancement with potentialobject or individual tracking applications. It recognizes the increasing importance of indoor positioning forlocation-based services. It anticipates future developments while acknowledging challenges such as multipathinterference, noise, data standardization, and scarcity of labeled data. This research contributes significantly toindoor localization technology, offering adaptability, device independence, and multifaceted DL-based solutionsfor real-world challenges and future advancements. Thus, the proposed work addresses challenges in objectlocalization precision and introduces a novel hybrid deep learning approach, contributing to advancing locationcentricservices.While deep learning-based indoor localization techniques have improved accuracy, challenges likedata noise, standardization, and availability of training data persist. However, ongoing developments are expectedto enhance indoor positioning systems to meet real-world demands.

Seropositivity and Other Determinants Associated with Toxoplasmosis in Local Buffalo in Iraq

A cross-sectional study was conducted to determine the Seropositivity of Toxoplasma gondii in water buffalo in three Iraqi governorates (Baghdad, Dhi Qar, and Maysan) and to estimate the risk aspects related to infestation throughout the period from January to December 2019. A total of 430 serum samples were inspected with a commercial ELISA (Enzyme linked immunosorbent assay) kit. Indirect multi-species kit. The overall Seropositivity of T. gondii in the examined local buffalo was 7.4%, and the highest rate (9.3%) was in Baghdad Governorate. A multivariate regression analysis revealed that adult buffalo (OR = 7.10;95% CI: 0.87-57.68;P = 0.067) and young herds (OR = 8.42;95% CI: 1.07-66.02;P = 0.043) were more subject to infestation from young buffalo and large herds. Furthermore, the hazard of toxoplasmosis was increased in winter especially among animals in contact with cats. It is therefore requisite to determine risk aspects to evaluate which mitigation, control, prevention and procedures should be carried out to diminish, control and prevent infestation with T. gondii and its propagation.

A process-oriented approach for identifying potential landslides considering time-dependent behaviors beyond geomorphological features

Geomorphological features are commonly used to identify potential landslides.Nevertheless,overemphasis on these features could lead to misjudgment.This research proposes a process-oriented approach for potential landslide identification that considers time-dependent behaviors.The method integrates comprehensive remote sensing and geological analysis to qualitatively assess slope stability,and employs numerical analysis to quantitatively calculate aging stability.Specifically,a time-dependent stability calculation method for anticlinal slopes is developed and implemented in discrete element software,incorporating time-dependent mechanical and strength reduction calculations.By considering the time-dependent evolution of slopes,this method highlights the importance of both geomorphological features and time-dependent behaviors in landslide identification.This method has been applied to the Jiarishan slope(JRS)on the Qinghai-Tibet Plateau as a case study.The results show that the JRS,despite having landslide geomorphology,is a stable slope,highlighting the risk of misjudgment when relying solely on geomorphological features.This work provides insights into the geomorphological characterization and evolution history of the JRS and offers valuable guidance for studying slopes with similar landslide geomorphology.Furthermore,the process-oriented method incorporating timedependent evolution provides a means to evaluate potential landslides,reducing misjudgment due to excessive reliance on geomorphological features.

Improved PSO-Extreme Learning Machine Algorithm for Indoor Localization

Wi Fi and fingerprinting localization method have been a hot topic in indoor positioning because of their universality and location-related features.The basic assumption of fingerprinting localization is that the received signal strength indication(RSSI)distance is accord with the location distance.Therefore,how to efficiently match the current RSSI of the user with the RSSI in the fingerprint database is the key to achieve high-accuracy localization.In this paper,a particle swarm optimization-extreme learning machine(PSO-ELM)algorithm is proposed on the basis of the original fingerprinting localization.Firstly,we collect the RSSI of the experimental area to construct the fingerprint database,and the ELM algorithm is applied to the online stages to determine the corresponding relation between the location of the terminal and the RSSI it receives.Secondly,PSO algorithm is used to improve the bias and weight of ELM neural network,and the global optimal results are obtained.Finally,extensive simulation results are presented.It is shown that the proposed algorithm can effectively reduce mean error of localization and improve positioning accuracy when compared with K-Nearest Neighbor(KNN),Kmeans and Back-propagation(BP)algorithms.

Ab initio density response and local field factor of warm dense hydrogen

We present quasi-exact ab initio path integral Monte Carlo(PIMC)results for the partial static density responses and local field factors of hydrogen in the warm dense matter regime,from solid density conditions to the strongly compressed case.The full dynamic treatment of electrons and protons on the same footing allows us to rigorously quantify both electronic and ionic exchange–correlation effects in the system,and to compare the results with those of earlier incomplete models such as the archetypal uniform electron gas or electrons in a fixed ion snapshot potential that do not take into account the interplay between the two constituents.The full electronic density response is highly sensitive to electronic localization around the ions,and our results constitute unambiguous predictions for upcoming X-ray Thomson scattering experiments with hydrogen jets and fusion plasmas.All PIMC results are made freely available and can be used directly for a gamut of applications,including inertial confinement fusion calculations and the modeling of dense astrophysical objects.Moreover,they constitute invaluable benchmark data for approximate but computationally less demanding approaches such as density functional theory or PIMC within the fixed-node approximation.

Interplay between topology and localization on superconducting circuits

Topological insulators occupy a prominent position in the realm of condensed matter physics. Nevertheless, the presence of strong disorder has the potential to disrupt the integrity of topological states, leading to the localization of all states.This study delves into the intricate interplay between topology and localization within the one-dimensional Su–Schrieffer–Heeger(SSH) model, which incorporates controllable off-diagonal quasi-periodic modulations on superconducting circuits.Through the application of external alternating current(ac) magnetic fluxes, each transmon undergoes controlled driving,enabling independent tuning of all coupling strengths. Within a framework of this model, we construct comprehensive phase diagrams delineating regions characterized by extended topologically nontrivial states, critical localization, and coexisting topological and critical localization phases. The paper also addresses the dynamics of qubit excitations, elucidating distinct quantum state transfers resulting from the intricate interplay between topology and localization. Additionally, we propose a method for detecting diverse quantum phases utilizing existing experimental setups.

Dynamical localization in a non-Hermitian Floquet synthetic system

We investigate the non-Hermitian effects on quantum diffusion in a kicked rotor model where the complex kicking potential is quasi-periodically modulated in the time domain.The synthetic space with arbitrary dimension can be created by incorporating incommensurate frequencies in the quasi-periodical modulation.In the Hermitian case,strong kicking induces the chaotic diffusion in the four-dimension momentum space characterized by linear growth of mean energy.We find that the quantum coherence in deep non-Hermitian regime can effectively suppress the chaotic diffusion and hence result in the emergence of dynamical localization.Moreover,the extent of dynamical localization is dramatically enhanced by increasing the non-Hermitian parameter.Interestingly,the quasi-energies become complex when the non-Hermitian parameter exceeds a certain threshold value.The quantum state will finally evolve to a quasi-eigenstate for which the imaginary part of its quasi-energy is large most.The exponential localization length decreases with the increase of the non-Hermitian parameter,unveiling the underlying mechanism of the enhancement of the dynamical localization by nonHermiticity.

A GENERALIZED SCALAR AUXILIARY VARIABLE METHOD FOR THE TIME-DEPENDENT GINZBURG-LANDAU EQUATIONS

This paper develops a generalized scalar auxiliary variable(SAV)method for the time-dependent Ginzburg-Landau equations.The backward Euler method is used for discretizing the temporal derivative of the time-dependent Ginzburg-Landau equations.In this method,the system is decoupled and linearized to avoid solving the non-linear equation at each step.The theoretical analysis proves that the generalized SAV method can preserve the maximum bound principle and energy stability,and this is confirmed by the numerical result,and also shows that the numerical algorithm is stable.

Experimental Study of Local Scour Around Four Piles Under Different Attack Angles and Gap Ratios

In an effort to investigate and quantify the patterns of local scour,researchers embarked on an in-depth study using a systematic experimental approach.The research focused on the effects of local scour around a set of four piles,each subjected to different hydromechanical conditions.In particular,this study aimed to determine how different attack angles—the angles at which the water flow impinges on the piles,and gap ratios—the ratios of the spacing between the piles to their diameters,influence the extent and nature of scour.A comprehensive series of 35 carefully designed experiments were orchestrated,each designed to dissect the nuances in how the gap ratio and attack angle might contribute to changes in the local scour observed at the base of pile groups.During these experimental trials,a wealth of local scour data were collected to support the analysis.These data included precise topographic profiles of the sediment bed around the pile groups,as well as detailed scour time histories showing the evolution of scour at strategic feature points throughout the test procedure.The analysis of the experimental data provided interesting insights.The study revealed that the interplay between the gap ratio and the attack angle had a pronounced influence on the scouring dynamics of the pile groups.One of the key observations was that the initial phases of scour,particularly within the first hour of water flow exposure,were characterized by a sharp increase in the scour depth occurring immediately in front of the piles.After this initial rapid development,the scour depth transitioned to a more gradual change rate.In contrast,the scour topography around the piles continuously evolved.This suggests that sediment displacement and the associated sculpting of the seabed around pile foundations are sustained and progressive processes,altering the underwater landscape over time.The results of this empirical investigation have significant implications for the design and construction of offshore multi-pile foundations,providing a critical reference for engineers and designers to estimate the expected scour depth around such structures,which is an integral part of decisions regarding foundation design,selection of structural materials,and implementation of scour protection measures.

Layered metastructure containing freely-designed local resonators for wave attenuation

Combining periodic layered structure with three-dimensional cylindrical local resonators,a hybrid metastructure with improved wave isolation ability was designed and investigated through theoretical and numerical approaches.The metastructure is composed of periodic rubber layers and concrete layers embedded with three-dimensional resonators,which can be freely designed with multi local resonant frequencies to attenuate vibrations at required frequencies and widen the attenuation bandgap.The metastructure can also effectively attenuate seismic responses.Compared with layered rubber-based structures,the metastructure has more excellent wave attenuation effects with greater attenuation and wider bandgap.

基于Local Cascade Ensemble方法的胎儿健康自动分类

为更好地自动评估胎儿宫内状态,提出一种基于local cascade ensemble(LCE)方法的胎儿健康状态分类模型。选用UCI数据集,使用ADASYN方法对不平衡数据集进行填充平衡,接着结合随机森林算法对数据特征进行选择,最后使用LCE方法对胎儿状态进行自动分类。实验结果表明,所提出模型使用的方法平均准确率、精确率、召回率和F1分数分别达到了0.9554、0.9054、0.9557和0.9290,对比传统的机器学习算法能得到更好的分类效果,有效降低了误判率。

Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

Scenario Modeling-Aided AP Placement Optimization Method for Indoor Localization and Network Access

Owing to the ubiquity of wireless networks and the popularity of WiFi infrastructures,received signal strength(RSS)-based indoor localization systems have received much attention.The placement of access points(APs)significantly influences localization accuracy and network access.However,the indoor scenario and network access are not fully considered in previous AP placement optimization methods.This study proposes a practical scenario modelingaided AP placement optimization method for improving localization accuracy and network access.In order to reduce the gap between simulation-based and field measurement-based AP placement optimization methods,we introduce an indoor scenario modeling and Gaussian process-based RSS prediction method.After that,the localization and network access metrics are implemented in the multiple objective particle swarm optimization(MOPSO)solution,Pareto front criterion and virtual repulsion force are applied to determine the optimal AP placement.Finally,field experiments demonstrate the effectiveness of the proposed indoor scenario modeling method and RSS prediction model.A thorough comparison confirms the localization and network access improvement attributed to the proposed anchor placement method.

In-situ AFM and quasi-in-situ studies for localized corrosion in Mg-9Al-1Fe-(Gd) alloys under 3.5 wt.% NaCl environment

Revealing the localized corrosion process of Mg alloy is considered as one of the most significant ways for improving its corrosion resistance.The reliable monitor should be high distinguishability and real-time in liquid environment.Herein,Mg-9Al-1Fe and Mg-9Al-1Fe-1Gd alloys were designed to highlight the impact of intermetallic on the corrosion behaviour.In-situ AFM with a special electrolyte circulation system and quasi-in-situ SEM observation were used to monitor the corrosion process of the designed alloys.SEM-EDS and TEM-SAED were applied to identify the intermetallic in the designed alloys,and their volta potentials were measured by SKPFM.According to the real-time and real-space in-situ AFM monitor,the corrosion process consisted of dissolution of anodicα-Mg phase,accumulation of corrosion products around cathodic phase and shedding of some fine cathodic phase.Then,the localized corrosion process of Mg alloy was revealed combined with the results of the monitor of corrosion process and Volta potential difference.