Publications by authors named "Xiangdong Ding"

109 Publications

MicroRNA-222 Transferred From Semen Extracellular Vesicles Inhibits Sperm Apoptosis by Targeting .

Front Cell Dev Biol 2021 8;9:736864. Epub 2021 Nov 8.

National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Seminal plasma contains a large number of extracellular vesicles (EVs). However, the roles of these EVs and their interactions with sperm are not clear. To identify the important molecules affecting sperm motility in EVs, we analyzed RNA from seminal plasma EVs of boars with different sperm motility using whole-transcriptome sequencing and proteomic analysis. In total, 7 miRNAs, 67 lncRNAs, 126 mRNAs and 76 proteins were differentially expressed between the two groups. We observed that EV-miR-222 can obviously improve sperm motility. In addition, the results suggested that miR-222 was transferred into sperm by the EVs and that miR-222 affected sperm apoptosis by inhibiting the expression of and . The results of electron microscopy also showed that overexpression of miR-222 in EVs could reduce sperm apoptosis. The study of the whole transcriptomes and proteomes of EVs in boar semen revealed some miRNAs may play an important role in these EVs interactions with Duroc sperm, and the findings suggest that the release of miR-222 by semen EVs is an important mechanism by which sperm viability is maintained and sperm apoptosis is reduced. Our studies provide a new insight of miR-222 in EVs regulation for sperm motility and sperm apoptosis.
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http://dx.doi.org/10.3389/fcell.2021.736864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8607813PMC
November 2021

Atlas of Prenatal Hair Follicle Morphogenesis Using the Pig as a Model System.

Front Cell Dev Biol 2021 7;9:721979. Epub 2021 Oct 7.

National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.

The pig is an increasingly popular biomedical model, but only a few in depth data exist on its studies in hair follicle (HF) morphogenesis and development. Hence, the objective of this study was to identify the suitability of the pig as an animal model for human hair research. We performed a classification of pig HF morphogenesis stages and hair types. All four different hair types sampled from 17 different body parts in pig were similar to those of human. The Guard_2 sub-type was more similar to type II human scalp hair while Guard_1, Awl, Auchene, and Zigzag were similar to type I scalp hair. Based on morphological observation and marker gene expression of HF at 11 different embryonic days and six postnatal days, we classified pig HF morphogenesis development from E41 to P45 into three main periods - induction (E37-E41), organogenesis (E41-E85), and cytodifferentiation (>E85). Furthermore, we demonstrated that human and pig share high similarities in HF morphogenesis occurrence time (early/mid gestational) and marker gene expression patterns. Our findings will facilitate the study of human follicle morphogenesis and research on complex hair diseases and offer researchers a suitable model for human hair research.
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http://dx.doi.org/10.3389/fcell.2021.721979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529045PMC
October 2021

Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development.

Front Genet 2021 6;12:740036. Epub 2021 Oct 6.

Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Identifying epigenetic changes is essential for an in-depth understanding of phenotypic diversity and pigs as the human medical model for anatomizing complex diseases. Abnormal sperm DNA methylation can lead to male infertility, fetal development failure, and affect the phenotypic traits of offspring. However, the whole genome epigenome map in pig sperm is lacking to date. In this study, we profiled methylation levels of cytosine in three commercial pig breeds, Landrace, Duroc, and Large White using whole-genome bisulfite sequencing (WGBS). The results showed that the correlation of methylation levels between Landrace and Large White pigs was higher. We found that 1,040-1,666 breed-specific hypomethylated regions (HMRs) were associated with embryonic developmental and economically complex traits for each breed. By integrating reduced representation bisulfite sequencing (RRBS) public data of pig testis, 1743 conservated HMRs between sperm and testis were defined, which may play a role in spermatogenesis. In addition, we found that the DNA methylation patterns of human and pig sperm showed high similarity by integrating public data from WGBS and chromatin immunoprecipitation sequencing (ChIP-seq) in other mammals, such as human and mouse. We identified 2,733 conserved HMRs between human and pig involved in organ development and brain-related traits, such as (neuroligin 1) containing a conserved-HMR between human and pig. Our results revealed the similarities and diversity of sperm methylation patterns among three commercial pig breeds and between human and pig. These findings are beneficial for elucidating the mechanism of male fertility, and the changes in commercial traits that undergo strong selection.
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http://dx.doi.org/10.3389/fgene.2021.740036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8527042PMC
October 2021

Rippling Ferroic Phase Transition and Domain Switching In 2D Materials.

Adv Mater 2021 Oct 10:e2103469. Epub 2021 Oct 10.

State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an, 710049, China.

Ripples are a class of native structural defects widely existing in 2D materials. They originate from the out-of-plane flexibility of 2D materials introducing spatially evolving electronic structure and friction behavior. However, the effect of ripples on 2D ferroics has not been reported. Here a molecular dynamics study of the effect of ripples on the temperature-induced ferroic phase transition and stress-induced ferroic domain switching in ferroelastic-ferroelectric monolayer GeSe is presented. Ripples stabilize the short-range ferroic orders in the high-temperature phase with stronger ferroicity and longer lifetime, thereby increasing the transition temperature upon cooling. In addition, ripples significantly affect the domain switching upon loading, changing it from a highly correlated process into a ripple-driven localized one where ripples act as source of dynamical random stress. These results reveal the fundamental role of ripples on 2D ferroicity and provide theoretical guidance for ripple engineering of controlled phase transition and domain switching with potential applications in flexible 2D electronics.
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http://dx.doi.org/10.1002/adma.202103469DOI Listing
October 2021

Identification of key genes affecting porcine fat deposition based on co-expression network analysis of weighted genes.

J Anim Sci Biotechnol 2021 Aug 20;12(1):100. Epub 2021 Aug 20.

Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Background: Fat deposition is an important economic consideration in pig production. The amount of fat deposition in pigs seriously affects production efficiency, quality, and reproductive performance, while also affecting consumers' choice of pork. Weighted gene co-expression network analysis (WGCNA) is effective in pig genetic studies. Therefore, this study aimed to identify modules that co-express genes associated with fat deposition in pigs (Songliao black and Landrace breeds) with extreme levels of backfat (high and low) and to identify the core genes in each of these modules.

Results: We used RNA sequences generated in different pig tissues to construct a gene expression matrix consisting of 12,862 genes from 36 samples. Eleven co-expression modules were identified using WGCNA and the number of genes in these modules ranged from 39 to 3,363. Four co-expression modules were significantly correlated with backfat thickness. A total of 16 genes (RAD9A, IGF2R, SCAP, TCAP, SMYD1, PFKM, DGAT1, GPS2, IGF1, MAPK8, FABP, FABP5, LEPR, UCP3, APOF, and FASN) were associated with fat deposition.

Conclusions: RAD9A, TCAP, SMYD1, PFKM, GPS2, and APOF were the key genes in the four modules based on the degree of gene connectivity. Combining these results with those from differential gene analysis, SMYD1 and PFKM were proposed as strong candidate genes for body size traits. This study explored the key genes that regulate porcine fat deposition and lays the foundation for further research into the molecular regulatory mechanisms underlying porcine fat deposition.
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http://dx.doi.org/10.1186/s40104-021-00616-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8379819PMC
August 2021

A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs.

Front Genet 2021 2;12:629049. Epub 2021 Jul 2.

National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.

The body shape of a pig is the most direct production index, which can fully reflect the pig's growth status and is closely related to important economic traits. In this study, a genome-wide association study on seven body size traits, the body length (BL), height (BH), chest circumference (CC), abdominal circumference (AC), cannon bone circumference (CBC), rump width (RW), and chest width (CW), were conducted in Yorkshire pigs. Illumina Porcine 80K SNP chips were used to genotype 589 of 5,572 Yorkshire pigs with body size records, and then the chip data was imputed to sequencing data. After quality control of imputed sequencing data, 784,267 SNPs were obtained, and the averaged linkage disequilibrium ( ) was 0.191. We used the single-trait model and the two-trait model to conduct single-step genome wide association study (ssGWAS) on seven body size traits; a total of 198 significant SNPS were finally identified according to the -value and the contribution to the genetic variance of individual SNP. 11 candidate genes (, , , , , , , , , , and ) were found to be associated with body size traits in pigs; and jointly affect AC and CC, and jointly affect RW and CW. These genes are involved in the regulation of bone growth and development as well as the absorption of nutrients and are associated with obesity. is proposed as a strong candidate gene for body size traits because of its important function and high consistency with other studies regarding the regulation of body size traits. Our results could provide valuable information for pig breeding based on molecular breeding.
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http://dx.doi.org/10.3389/fgene.2021.629049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283822PMC
July 2021

Mutation Spectrum of From 21,324 Chinese Patients With Non-Small Cell Lung Cancer (NSCLC) Successfully Tested by Multiple Methods in a CAP-Accredited Laboratory.

Pathol Oncol Res 2021 7;27:602726. Epub 2021 Apr 7.

Clinical Genome Center, KingMed Diagnostics, Guangzhou, China.

Genotyping epidermal growth factor receptor () gene in patients with advanced non-small cell lung cancers (NSCLC) is essential for identifying those patients who may benefit from targeted therapies. Systemically evaluating mutation detection rates of different methods currently used in clinical setting will provide valuable information to clinicians and laboratory scientists who take care of NSCLC patients. This study retrospectively reviewed the data obtained in our laboratory in last 10 years. A total of 21,324 NSCLC cases successfully underwent genotyping for clinical therapeutic purpose, including 5,244 cases tested by Sanger sequencing, 13,329 cases tested by real-time PCR, and 2,751 tested by next-generation sequencing (NGS). The average mutation rate was 45.1%, with 40.3% identified by Sanger sequencing, 46.5% by real-time PCR and 47.5% by NGS. Of these cases with mutations identified, 93.3% of them harbored a single mutation (92.1% with 19del or L858R, and 7.9% with uncommon mutations) and 6.7% harbored complex mutations. Of the 72 distinct variants identified in this study, 15 of them (single or complex mutations) were newly identified in NSCLC. For these cases with mutations tested by NGS, 65.3% of them also carried tumor-related variants in some non- genes and about one third of them were considered candidates of targeted drugs. NGS method showed advantages over Sanger sequencing and real-time PCR not only by providing the highest mutation detection rate of but also by identifying actionable non- mutations with targeted drugs in clinical setting.
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http://dx.doi.org/10.3389/pore.2021.602726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262202PMC
April 2021

Twisting of a Pristine α-Fe Nanowire: From Wild Dislocation Avalanches to Mild Local Amorphization.

Nanomaterials (Basel) 2021 Jun 18;11(6). Epub 2021 Jun 18.

State Key Laboratory for Mechanical Behaviour of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China.

The torsion of pristine α-Fe nanowires was studied by molecular dynamics simulations. Torsion-induced plastic deformation in pristine nanowires is divided into two regimes. Under weak torsion, plastic deformation leads to dislocation nucleation and propagation. Twisting-induced dislocations are mainly 12<111> screw dislocations in a <112>-oriented nanowire. The nucleation and propagation of these dislocations were found to form avalanches which generate the emission of energy jerks. Their probability distribution function (PDF) showed power laws with mixing between different energy exponents. The mixing stemmed from simultaneous axial and radial dislocation movements. The power-law distribution indicated strongly correlated 'wild' dislocation dynamics. At the end of this regime, the dislocation pattern was frozen, and further twisting of the nanowire did not change the dislocation pattern. Instead, it induced local amorphization at the grip points at the ends of the sample. This "melting" generated highly dampened, mild avalanches. We compared the deformation mechanisms of twinned and pristine α-Fe nanowires under torsion.
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http://dx.doi.org/10.3390/nano11061602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8234800PMC
June 2021

Author Correction: Nanoscale bubble domains with polar topologies in bulk ferroelectrics.

Nat Commun 2021 Jun 24;12(1):4035. Epub 2021 Jun 24.

Department of Materials Science and Engineering, National University of Singapore, Singapore City, Singapore.

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http://dx.doi.org/10.1038/s41467-021-24356-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8225867PMC
June 2021

Nanoscale bubble domains with polar topologies in bulk ferroelectrics.

Nat Commun 2021 Jun 15;12(1):3632. Epub 2021 Jun 15.

Department of Materials Science and Engineering, National University of Singapore, Singapore City, Singapore.

Multitudinous topological configurations spawn oases of many physical properties and phenomena in condensed-matter physics. Nano-sized ferroelectric bubble domains with various polar topologies (e.g., vortices, skyrmions) achieved in ferroelectric films present great potential for valuable physical properties. However, experimentally manipulating bubble domains has remained elusive especially in the bulk form. Here, in any bulk material, we achieve self-confined bubble domains with multiple polar topologies in bulk BiNaTiO ferroelectrics, especially skyrmions, as validated by direct Z-contrast imaging. This phenomenon is driven by the interplay of bulk, elastic and electrostatic energies of coexisting modulated phases with strong and weak spontaneous polarizations. We demonstrate reversable and tip-voltage magnitude/time-dependent donut-like domain morphology evolution towards continuously and reversibly modulated high-density nonvolatile ferroelectric memories.
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http://dx.doi.org/10.1038/s41467-021-23863-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8206216PMC
June 2021

Alkali-deficiency driven charged out-of-phase boundaries for giant electromechanical response.

Nat Commun 2021 May 14;12(1):2841. Epub 2021 May 14.

Department of Materials Science and Engineering, National University of Singapore, Singapore, Singapore.

Traditional strategies for improving piezoelectric properties have focused on phase boundary engineering through complex chemical alloying and phase control. Although they have been successfully employed in bulk materials, they have not been effective in thin films due to the severe deterioration in epitaxy, which is critical to film properties. Contending with the opposing effects of alloying and epitaxy in thin films has been a long-standing issue. Herein we demonstrate a new strategy in alkali niobate epitaxial films, utilizing alkali vacancies without alloying to form nanopillars enclosed with out-of-phase boundaries that can give rise to a giant electromechanical response. Both atomically resolved polarization mapping and phase field simulations show that the boundaries are strained and charged, manifesting as head-head and tail-tail polarization bound charges. Such charged boundaries produce a giant local depolarization field, which facilitates a steady polarization rotation between the matrix and nanopillars. The local elastic strain and charge manipulation at out-of-phase boundaries, demonstrated here, can be used as an effective pathway to obtain large electromechanical response with good temperature stability in similar perovskite oxides.
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http://dx.doi.org/10.1038/s41467-021-23107-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121868PMC
May 2021

2.4  kW 1045  nm narrow-spectral-width monolithic single-mode CW fiber laser by using an FBG-based MOPA configuration.

Appl Opt 2021 May;60(13):3740-3746

A 24 kW narrow-spectral-width near-diffraction-limited monolithic fiber laser system at ${\sim}{1045.2}\;{\rm{nm}}$ in a fiber Bragg grating (FBG)-based master oscillator power amplifier (MOPA) configuration is demonstrated in this paper. The near-diffraction-limited beam quality (${{\rm{M}}^2}\sim{1.2}$) and a spectral width of 0.35 nm (${\sim}{{96}}\;{\rm{GHz}}$) are achieved. The stimulated Raman scattering (SRS) is theoretically and experimentally investigated. The SRS has been suppressed by carefully optimizing the length of the Yb-doped fiber and the pumping scheme, and a signal-to-noise ratio of ${\sim}{{33}}\;{\rm{dB}}$ between the laser signal and the Raman Stokes component is achieved. The stimulate Brillouin scattering and the transverse mode instability are not observed. To our best knowledge, this is the highest-output power for ${{104}} \times {\rm{nm}}$ single-mode fiber laser with ${\sim}{{96}}\;{\rm{GHz}}$ spectral width by using an FBG-based MOPA configuration.
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http://dx.doi.org/10.1364/AO.420708DOI Listing
May 2021

Genomic Prediction Using Bayesian Regression Models With Global-Local Prior.

Front Genet 2021 15;12:628205. Epub 2021 Apr 15.

National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Bayesian regression models are widely used in genomic prediction for various species. By introducing the global parameter τ, which can shrink marker effects to zero, and the local parameter λ , which can allow markers with large effects to escape from the shrinkage, we developed two novel Bayesian models, named BayesHP and BayesHE. The BayesHP model uses Horseshoe+ prior, whereas the BayesHE model assumes local parameter λ , after a half-t distribution with an unknown degree of freedom. The performances of BayesHP and BayesHE models were compared with three classical prediction models, including GBLUP, BayesA, and BayesB, and BayesU, which also applied global-local prior (Horseshoe prior). To assess model performances for traits with various genetic architectures, simulated data and real data in cattle (milk production, health, and type traits) and mice (type and growth traits) were analyzed. The results of simulation data analysis indicated that models based on global-local priors, including BayesU, BayesHP, and BayesHE, performed better in traits with higher heritability and fewer quantitative trait locus. The results of real data analysis showed that BayesHE was optimal or suboptimal for all traits, whereas BayesHP was not superior to other classical models. For BayesHE, its flexibility to estimate hyperparameter automatically allows the model to be more adaptable to a wider range of traits. The BayesHP model, however, tended to be suitable for traits having major/large quantitative trait locus, given its nature of the "U" type-like shrinkage pattern. Our results suggested that auto-estimate the degree of freedom (e.g., BayesHE) would be a better choice other than increasing the local parameter layers (e.g., BayesHP). In this study, we introduced the global-local prior with unknown hyperparameter to Bayesian regression models for genomic prediction, which can trigger further investigations on model development.
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http://dx.doi.org/10.3389/fgene.2021.628205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8083873PMC
April 2021

Integrative analysis of genome-wide DNA methylation and gene expression profiles reveals important epigenetic genes related to milk production traits in dairy cattle.

J Anim Breed Genet 2021 Sep 23;138(5):562-573. Epub 2021 Feb 23.

Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Epigenetic modification plays a critical role in establishing and maintaining cell differentiation, embryo development, tumorigenesis and many complex diseases. However, little is known about the epigenetic regulatory mechanisms for milk production in dairy cattle. Here, we conducted an epigenome-wide study, together with gene expression profiles to identify important epigenetic candidate genes related to the milk production traits in dairy cattle. Whole-genome bisulphite sequencing and RNA sequencing were employed to detect differentially methylated genes (DMG) and differentially expressed genes (DEG) in blood samples in dry period and lactation period between two groups of cows with extremely high and low milk production performance. A total of 10,877 and 6,617 differentially methylated regions were identified between the two groups in the two periods, which corresponded to 3,601 and 2,802 DMGs, respectively. Furthermore, 156 DEGs overlap with DMGs in comparison of the two groups, and 131 DEGs overlap with DMGs in comparison of the two periods. By integrating methylome, transcriptome and GWAS data, some potential candidate genes for milk production traits in dairy cattle were suggested, such as DOCK1, PTK2 and PIK3R1. Our studies may contribute to a better understanding of epigenetic modification on milk production traits of dairy cattle.
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http://dx.doi.org/10.1111/jbg.12530DOI Listing
September 2021

Determining Multi-Component Phase Diagrams with Desired Characteristics Using Active Learning.

Adv Sci (Weinh) 2020 Jan 23;8(1):2003165. Epub 2020 Nov 23.

Los Alamos National Laboratory Los Alamos New Mexico 87545 USA.

Herein, we demonstrate how to predict and experimentally validate phase diagrams for multi-component systems from a high-dimensional virtual space of all possible phase diagrams involving several elements based on small existing experimental data. The experimental data for bulk phases for known systems represents a sampling from this space, and screening the space allows multi-component phase diagrams with given design criteria to be built. This approach uses machine learning methods to predict phase diagrams and Bayesian experimental design to minimize experiments for refinement and validation, all within an active learning loop. The approach is proven by predicting and synthesizing the ferroelectric ceramic system (1-)(BaCaSrTiO)-(BaTiZrSnHfO) with a relatively high transition temperature and triple point, as well as the NiTi-based pseudo-binary phase diagram (1-)(TiNiHfZr)-(TiNiHfZrNb) designed for high transition temperature ( ⩽ 1). Each phase diagram is validated and optimized through only three new experiments. The complexity of these compounds is beyond the reach of today's computational methods.
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http://dx.doi.org/10.1002/advs.202003165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788591PMC
January 2020

Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies.

Genome Biol Evol 2021 01;13(1)

Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.

The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.
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http://dx.doi.org/10.1093/gbe/evaa231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7850101PMC
January 2021

Periodic Wrinkle-Patterned Single-Crystalline Ferroelectric Oxide Membranes with Enhanced Piezoelectricity.

Adv Mater 2020 Dec 2;32(50):e2004477. Epub 2020 Nov 2.

The Electronic Materials Research Laboratory, Key Laboratory of the Ministry of Education & International Center for Dielectric Research, School of Electronic Science and Engineering, State Key Laboratory for Mechanical Behavior of Materials, the International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technology, Xi'an Jiaotong University, Xi'an, 710049, China.

Self-assembled membranes with periodic wrinkled patterns are the critical building blocks of various flexible electronics, where the wrinkles are usually designed and fabricated to provide distinct functionalities. These membranes are typically metallic and organic materials with good ductility that are tolerant of complex deformation. However, the preparation of oxide membranes, especially those with intricate wrinkle patterns, is challenging due to their inherently strong covalent or ionic bonding, which usually leads to material crazing and brittle fracture. Here, wrinkle-patterned BaTiO (BTO)/poly(dimethylsiloxane) membranes with finely controlled parallel, zigzag, and mosaic patterns are prepared. The BTO layers show excellent flexibility and can form well-ordered and periodic wrinkles under compressive in-plane stress. Enhanced piezoelectricity is observed at the sites of peaks and valleys of the wrinkles where the largest strain gradient is generated. Atomistic simulations further reveal that the excellent elasticity and the correlated coupling between polarization and strain/strain gradient are strongly associated with ferroelectric domain switching and continuous dipole rotation. The out-of-plane polarization is primarily generated at compressive regions, while the in-plane polarization dominates at the tensile regions. The wrinkled ferroelectric oxides with differently strained regions and correlated polarization distributions would pave a way toward novel flexible electronics.
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http://dx.doi.org/10.1002/adma.202004477DOI Listing
December 2020

The superiority of multi-trait models with genotype-by-environment interactions in a limited number of environments for genomic prediction in pigs.

J Anim Sci Biotechnol 2020 19;11:88. Epub 2020 Aug 19.

National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China.

Background: Different production systems and climates could lead to genotype-by-environment (G × E) interactions between populations, and the inclusion of G × E interactions is becoming essential in breeding decisions. The objective of this study was to investigate the performance of multi-trait models in genomic prediction in a limited number of environments with G × E interactions.

Results: In total, 2,688 and 1,384 individuals with growth and reproduction phenotypes, respectively, from two Yorkshire pig populations with similar genetic backgrounds were genotyped with the PorcineSNP80 panel. Single- and multi-trait models with genomic best linear unbiased prediction (GBLUP) and BayesC were implemented to investigate their genomic prediction abilities with 20 replicates of five-fold cross-validation. Our results regarding between-environment genetic correlations of growth and reproductive traits (ranging from 0.618 to 0.723) indicated the existence of G × E interactions between these two Yorkshire pig populations. For single-trait models, genomic prediction with GBLUP was only 1.1% more accurate on average in the combined population than in single populations, and no significant improvements were obtained by BayesC for most traits. In addition, single-trait models with either GBLUP or BayesC produced greater bias for the combined population than for single populations. However, multi-trait models with GBLUP and BayesC better accommodated G × E interactions, yielding 2.2% - 3.8% and 1.0% - 2.5% higher prediction accuracies for growth and reproductive traits, respectively, compared to those for single-trait models of single populations and the combined population. The multi-trait models also yielded lower bias and larger gains in the case of a small reference population. The smaller improvement in prediction accuracy and larger bias obtained by the single-trait models in the combined population was mainly due to the low consistency of linkage disequilibrium between the two populations, which also caused the BayesC method to always produce the largest standard error in marker effect estimation for the combined population.

Conclusions: In conclusion, our findings confirmed that directly combining populations to enlarge the reference population is not efficient in improving the accuracy of genomic prediction in the presence of G × E interactions, while multi-trait models perform better in a limited number of environments with G × E interactions.
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http://dx.doi.org/10.1186/s40104-020-00493-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7507970PMC
August 2020

Optimizing genomic prediction model given causal genes in a dairy cattle population.

J Dairy Sci 2020 Nov 18;103(11):10299-10310. Epub 2020 Sep 18.

Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China. Electronic address:

As genotypic data are moving from SNP chip toward whole-genome sequence, the accuracy of genomic prediction (GP) exhibits a marginal gain, although all genetic variation, including causal genes, are contained in whole-genome sequence data. Meanwhile, genetic analyses on complex traits, such as genome-wide association studies, have identified an increasing number of genomic regions, including potential causal genes, which would be reliable prior knowledge for GP. Many studies have tried to improve the performance of GP by modifying the prediction model to incorporate prior knowledge. Although several plausible results have been obtained from model modification or strategy optimization, most of them were validated in a specific empirical population with a limited variety of genetic architecture for complex traits. An alternative approach is to use simulated genetic architecture with known causal genes (e.g., simulated causative SNP) to evaluate different GP models with given causal genes. Our objectives were to (1) evaluate the performance of GP under a variety of genetic architectures with a subset of known causal genes and (2) compare different GP models modified by highlighting causal genes and different strategies to weight causal genes. In this study, we simulated pseudo-phenotypes under a variety of genetic architectures based on the real genotypes and phenotypes of a dairy cattle population. Besides classical genomic best linear unbiased prediction, we evaluated 3 modified GP models that highlight causal genes as follows: (1) by treating them as fixed effects, (2) by treating them as a separate random component, and (3) by combining them into the genomic relationship matrix as random effects. Our results showed that highlighting the known causal genes, which explained a considerable proportion of genetic variance in the GP models, increased the predictive accuracy. Combining all given causal genes into the genomic relationship matrix was the optimal strategy under all the scenarios validated, and treating causal genes as a separate random component is also recommended, when more than 20% of genetic variance was explained by known causal genes. Moreover, assigning differential weights to each causal gene further improved the predictive accuracy.
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http://dx.doi.org/10.3168/jds.2020-18233DOI Listing
November 2020

Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds.

Animals (Basel) 2020 Sep 11;10(9). Epub 2020 Sep 11.

Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.

Selection signature provides an efficient tool to explore genes related to traits of interest. In this study, 176 ewes from one Chinese uniparous breed and three Kazakhstan multiparous breeds are genotyped using Affymetrix 600K HD single nucleotide polymorphism (SNP) arrays, F-statistics (Fst), and a Cross Population Extend Haplotype Homozygosity Test (XPEHH). These are conducted to identify genomic regions that might be under selection in three population pairs comprised the one multiparous breed and the uniparous breed. A total of 177 and 3072 common selective signatures were identified by Fst and XPEHH test, respectively. Nearly half of the common signatures detected by Fst were also captured by XPEHH test. In addition, 1337 positive and 1735 common negative signatures were observed by XPEHH in three Kazakhstan multiparous breeds. In total, 242 and 798 genes were identified in selective regions and positive selective regions identified by Fst and XPEHH, respectively. These genes were further clustered in 50 gene ontology (GO) functional terms and 66 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in enrichment analysis. The GO terms and pathways were relevant with reproductive processes, e.g., oxytocin signaling pathway, thyroid hormone synthesis and GnRH signaling pathway, vascular smooth muscle contraction and lipid metabolism (alpha-Linolenic acid metabolism and Linoleic acid metabolism), etc. Based on the findings, six potential candidate genes , , , , , and , under positive selection related to characteristics of multiparous sheep breeds were revealed. Our results improve our understanding of the mechanisms of selection that underlies the prolificacy trait in sheep, and provide essential references for future sheep breeding.
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http://dx.doi.org/10.3390/ani10091633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552267PMC
September 2020

Knowledge-Based Descriptor for the Compositional Dependence of the Phase Transition in BaTiO-Based Ferroelectrics.

ACS Appl Mater Interfaces 2020 Oct 24;12(40):44970-44980. Epub 2020 Sep 24.

Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.

Descriptors play a central role in constructing composition-structure-property relationships to guide materials design. We propose a material descriptor, δτ, for the composition dependence of the Curie temperature () on single doping elements in BaTiO ferroelectrics, which is then generalized to a linear combination of multiple dopants in the solid solutions. The descriptor δτ depends linearly on the Curie temperature and also serves to separate the ferroelectric phase from the relaxor phase. We compare δτ to other commonly used descriptors such as the tolerance factor, electronegativity, and ionic displacement. By using regression analysis on our assembled experimental data, we show how it outperforms other descriptors. We use the trained machine-learned models to predict compositions in our search space with the largest ferroelectric, dielectric, and piezoelectric properties, namely, , electrostrain, and recoverable energy storage density. We experimentally verify our predictions for and classification into ferroelectrics and relaxors by synthesizing and characterizing six solid solutions in BaTiO ferroelectrics. Our definition of δτ can shed light on the design of knowledge-based descriptors in other systems such as Pb-based and Bi-based solid solutions.
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http://dx.doi.org/10.1021/acsami.0c12763DOI Listing
October 2020

Genomic prediction of growth traits for pigs in the presence of genotype by environment interactions using single-step genomic reaction norm model.

J Anim Breed Genet 2020 Nov 11;137(6):523-534. Epub 2020 Aug 11.

National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China.

Economically important traits are usually complex traits influenced by genes, environment and genotype-by-environment (G × E) interactions. Ignoring G × E interaction could lead to bias in the estimation of breeding values and selection decisions. A total of 1,778 pigs were genotyped using the PorcineSNP80 BeadChip. The existence of G × E interactions was investigated using a single-step reaction norm model for growth traits of days to 100 kg (AGE) and backfat thickness adjusted to 100 kg (BFT), based on a pedigree-based relationship matrix (A) or a genomic-pedigree joint relationship matrix (H). In the reaction norm model, the herd-year-season effect was measured as the environmental variable (EV). Our results showed no G × E interactions for AGE, but for BFT. For both AGE and BFT, the genomic reaction norm model (H) produced more accurate predictions than the conventional reaction norm model (A). For BFT, the accuracies were greater based on the reaction norm model than those based on the reduced model without exploiting G × E interaction, with EV ranging from 0.5 to 1, and accuracy increasing by 3.9% and 4.6% in the reaction norm model based on A and H matrices, respectively, while reaction norm model yielded approximately 8.4% and 7.9% lower accuracy for EVs ranging from 0 to 0.4, based on A and H matrices, respectively. In addition, for BFT, the highest accuracy was obtained in the BJLM6 farm for realizing directional selection. This study will help to apply G × E interactions to practical genomic selection.
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http://dx.doi.org/10.1111/jbg.12499DOI Listing
November 2020

A Genome-Wide Association Study on Feed Efficiency Related Traits in Landrace Pigs.

Front Genet 2020 3;11:692. Epub 2020 Jul 3.

National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Feed efficiency (FE) traits in pigs are of utmost economic importance. Genetic improvement of FE related traits in pigs might significantly reduce production cost and energy consumption. Hence, our study aimed at identifying SNPs and candidate genes associated with FE related traits, including feed conversion ratio (FCR), average daily gain (ADG), average daily feed intake (ADFI), and residual feed intake (RFI). A genome-wide association study (GWAS) was performed for the four FE related traits in 296 Landrace pigs genotyped with PorcineSNP50 BeadChip. Two different single-trait methods, single SNP linear model GWAS (LM-GWAS) and single-step GWAS (ssGWAS), were implemented. Our results showed that the two methods showed high consistency with respect to SNP identification. A total of 32 common significant SNPs associated with the four FE related traits were identified. Bioinformatics analysis revealed eight common QTL regions, of which three QTL regions related to ADFI and RFI traits were overlapped. Gene ontology analysis revealed six common candidate genes () relevant for the four FE related traits. These genes are involved in the processes of fat synthesis and decomposition, lipid transport process, insulin metabolism, among others. Our results provide, new insights into the genetic mechanisms and candidate function genes of FE related traits in pigs. However, further investigations to validate these results are warranted.
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http://dx.doi.org/10.3389/fgene.2020.00692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350416PMC
July 2020

Unusual activated processes controlling dislocation motion in body-centered-cubic high-entropy alloys.

Proc Natl Acad Sci U S A 2020 Jul 29;117(28):16199-16206. Epub 2020 Jun 29.

Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218

Atomistic simulations of dislocation mobility reveal that body-centered cubic (BCC) high-entropy alloys (HEAs) are distinctly different from traditional BCC metals. HEAs are concentrated solutions in which composition fluctuation is almost inevitable. The resultant inhomogeneities, while locally promoting kink nucleation on screw dislocations, trap them against propagation with an appreciable energy barrier, replacing kink nucleation as the rate-limiting mechanism. Edge dislocations encounter a similar activated process of nanoscale segment detrapping, with comparable activation barrier. As a result, the mobility of edge dislocations, and hence their contribution to strength, becomes comparable to screw dislocations.
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http://dx.doi.org/10.1073/pnas.1919136117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368262PMC
July 2020

Charge doping induced reversible multistep structural phase transitions and electromechanical actuation in two-dimensional 1T'-MoS.

Nanoscale 2020 Jun;12(23):12541-12550

Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia.

The 1T' phase of transition metal dichalcogenides (TMDs) is a low symmetry charge density wave (CDW) phase, which can be viewed as a periodically distorted structure (Peierls distortion) of the high symmetry 1T phase. In this paper, using density functional theory (DFT) calculations, we report that the positive charge (hole) injection is an effective method to modulate the Peierls distortion of MoS2 1T' for a new CDW phase and superior electromechanical properties. A new stable CDW phase is discovered at a hole doping level of 0.10 h+ per atom, named 1T't. Hole charging and discharging can induce a reversible phase transition of MoS2 among the three phases, 1T, 1T' and 1T't. Such a reversible phase transition leads to superior electromechanical properties including a strain output as high as -5.8% with a small hysteresis loop, multi-step super-elasticity, and multi-shape memory effect, which are valuable in active electromechanical device designs at the nanoscale. In-depth analysis of the change of the electronic structure under hole doping was performed to understand the new CDW phase and the observed phase transition. Using charge doping to modulate the Peierls distortion in two-dimensional materials can serve as a general concept for nano-active material designs.
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http://dx.doi.org/10.1039/d0nr02049dDOI Listing
June 2020

An ultrathin two-dimensional vertical ferroelectric tunneling junction based on CuInPS monolayer.

Nanoscale 2020 Jun;12(23):12522-12530

Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi' an 710049, People's Republic of China.

Ferroelectric (FE) materials, especially ABO3 FE perovskite oxides, have been extensively studied for their important applications in memory devices, electronics and sensors. However, the integration of FE perovskite oxides into miniaturized memory and electronic devices has been impeded by the critical thickness limitation, as out-of-plane ferroelectricity in most FE perovskite oxides will disappear when the oxide thin film thickness is below a critical value. On the other side, CuInP2S6 (CIPS) nano-flake, a prototypical two-dimensional (2D) FE material, has recently been demonstrated to display stable out-of-plane ferroelectricity at the atomic layer thickness by experiment, which offers a new candidate for developing FE devices in the 2D nanoscale regime. Herein, after investigation of the structural and ferroelectric properties of 2D CIPS layers, especially the interactions between out-of-plane polarization and the corresponding depolarization field using first-principles calculations, we reveal that out-of-plane ferroelectricity can even persist in the CIPS monolayer, which is only 3.4 Å in thickness. Moreover, in order to explore the potential application of 2D FE CIPS layers as minimized FE devices, we design an ultrathin ferroelectric tunneling junction (FTJ) composed of a graphene/CIPS monolayer/graphene vertical van der Waals (vdW) heterostructure. Our transport simulations based on the non-equilibrium Green's function formalism predict that such an ultrathin FTJ device can still exhibit the typical tunneling electroresistance (TER) effect, where tunneling current strongly depends on the direction of FE polarization. Our work not only elucidates the origin of stable out-of-plane ferroelectricity appearing in 2D CIPS layers, but also demonstrates the practical application of a CIPS based 2D FTJ as a miniaturized, multi-functional and low-power consumption memory device for modern electronics.
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http://dx.doi.org/10.1039/d0nr01475cDOI Listing
June 2020

Effect of active cycle of breathing techniques in patients with chronic obstructive pulmonary disease: a systematic review of intervention.

Eur J Phys Rehabil Med 2020 Oct 13;56(5):625-632. Epub 2020 May 13.

Department of Respiratory Medicine, Jilin University First Hospital, Changchun, China.

Introduction: Patients with chronic obstructive pulmonary disease (COPD) often suffer from expectoration. To address this problem, active cycle of breathing techniques (ACBT) can be applied. However, the effects of ACBT on COPD patients have shown mixed results. Therefore, we investigated the effectiveness of ACBT in patients with COPD by conducting a systematic review of the literature.

Evidence Acquisition: Seven electronic databases (PubMed, Web of Science, Embase, CINAHL, China National Knowledge Infrastructure [CNKI], Chinese Biomedical Literature [CBM], and Wanfang Database) were carefully searched from August 17th to 19th, 2019.

Evidence Synthesis: The search yielded 2224 records, and ultimately only eight articles were selected for analysis. A total of 390 patients were included in the eight studies. The intervention program is a comparison of ACBT with non-ACBT. For COPD patients, ACBT was more effective in sputum production and cough efficiency. Compared with usual care, ACBT may improve lung function, blood gas analysis, and other parameters.

Conclusions: Our systematic review found that ACBT can effectively improve the sputum production and cough efficiency in patients with COPD. However, there was no definite conclusion on the effectiveness of ACBT on lung function, blood gas analysis and other aspects. More research and quantitative analyses are needed to confirm the effectiveness of ACBT on other aspects of COPD patient.
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http://dx.doi.org/10.23736/S1973-9087.20.06144-4DOI Listing
October 2020

A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds.

Asian-Australas J Anim Sci 2020 Sep 21;33(9):1400-1410. Epub 2019 Oct 21.

National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.

Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB).

Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multitrait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874).

Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits.

Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.
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http://dx.doi.org/10.5713/ajas.19.0411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7468174PMC
September 2020

Porcine Epidemic Diarrhea Altered Colonic Microbiota Communities in Suckling Piglets.

Genes (Basel) 2019 12 30;11(1). Epub 2019 Dec 30.

Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.

Porcine epidemic diarrhea (PED) is a major gastrointestinal disease afflicting suckling pigs that causes huge industrial economic losses. In this study, we investigated microbiota from the colonic mucosa and content in healthy and PED piglets. High-throughput 16S rRNA gene sequencing was performed to identify inter-group differences. Firmicutes, Fusobacteria, Proteobacteria, and Bacteroidetes were the top four affected phyla. The proportion of Proteobacteria was higher in infected than in healthy piglets, and the opposite was observed for Bacteroidetes (more than four-fold higher in the healthy group). In the infected group, accounted for 36.56% and 21.61% in the colonic mucosa and contents, respectively, while in the healthy group, they comprised 22.53% and 12.67%, respectively. The percentage of in healthy colons (15.63%) was considerably higher than that in the disease group (<10%). In both the colonic mucosa and contents, functional enrichment differed significantly between healthy and diseased groups. Overall, infection with the PED virus increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria in the colons of piglets. Targeting intestinal microbiota could be a promising method for PED prevention, thus opening new avenues for future research.
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http://dx.doi.org/10.3390/genes11010044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016528PMC
December 2019

Generalized Stacking Fault Energy of Al-Doped CrMnFeCoNi High-Entropy Alloy.

Nanomaterials (Basel) 2019 Dec 26;10(1). Epub 2019 Dec 26.

Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology, SE-100 44 Stockholm, Sweden.

Using first-principles methods, we investigate the effect of Al on the generalized stacking fault energy of face-centered cubic (fcc) CrMnFeCoNi high-entropy alloy as a function of temperature. Upon Al addition or temperature increase, the intrinsic and extrinsic stacking fault energies increase, whereas the unstable stacking fault and unstable twinning fault energies decrease monotonously. The thermodynamic expression for the intrinsic stacking fault energy in combination with the theoretical Gibbs energy difference between the hexagonal close packed (hcp) and fcc lattices allows one to determine the so-called hcp-fcc interfacial energy. The results show that the interfacial energy is small and only weakly dependent on temperature and Al content. Two parameters are adopted to measure the nano-twinning ability of the present high-entropy alloys (HEAs). Both measures indicate that the twinability decreases with increasing temperature or Al content. The present study provides systematic theoretical plasticity parameters for modeling and designing high entropy alloys with specific mechanical properties.
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http://dx.doi.org/10.3390/nano10010059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7022399PMC
December 2019
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