Search Results (12)

Background/Objectives: Kinship inference is commonly adopted in various forensic applications, but previous studies have often lacked precision. Methods: In this study, a new method for the nomenclature of kinship types, i.e., kinship chain (KC), was proposed, and then, six types of identity by state (IBS) scores were calculated for simulated and real families using four types of markers. Finally, several Bayesian network (BN)-based classifiers were constructed to investigate the efficiency of the kinship inference. Results: A total of 7, 22, 58, and 3 KCs were obtained for common first-, second-, and third-degree relatives and unrelated pairs, respectively. High accuracies could be achieved in distinguishing between related and unrelated pairs after combining the four types of genetic markers, with an accuracy of >99.99% for all 7 KCs of first-degree relationships and ~99% for 14 out of 22 KCs of second-degree relatives. When comparing relationships of the same degree, the accuracies were 99.28%, 42.31%, and 15.82% for first-, second-, and third-degree relationships, respectively. When it came to differentiating unspecific relationships, the overall accuracy was over 80%. All the results were validated on real family data. Conclusions: With the new nomenclature method of kinship types and the combination of autosomal and non-autosomal genetic markers, kinship inference can be realized with high accuracy and precision, which will be helpful in complex forensic cases, such as the identification of mass disaster victims. Full article

Background: Beagle dogs are widely used in biomedical research, but their genetic diversity and population structure require further investigation. This study aimed to assess genetic diversity, population structure, and selection signals in a foundational Beagle breeding population using genome-wide SNP genotyping. Methods: A total of 459 Beagle dogs (108 males, 351 females) were genotyped using the Canine 50K SNP chip. After quality control, 456 individuals and 31,198 SNPs were retained. Genetic diversity indices, principal component analysis (PCA), identity-by-state (IBS) distance, a genomic relationship matrix (G-matrix), runs of homozygosity (ROH), and Tajima’s D selection scans were analyzed. Results: The average minor allele frequency was 0.224, observed heterozygosity was 0.303, and expected heterozygosity was 0.305. A total of 2990 ROH segments were detected, with a mean inbreeding coefficient of 0.031. Phylogenetic analysis classified 106 stud dogs into 13 lineages. Selection signal analysis identified TTN (muscle function) and DLA-DRA, DLA-DOA, DLA-DMA (immune regulation) under selection. Conclusions: The Beagle population exhibits high genetic diversity and low inbreeding. To maintain genetic stability and ensure the long-term conservation of genetic resources, structured breeding strategies should be implemented based on lineage classifications. Full article

The significance of the chiral symmetry restoration is studied by considering the role of the modification of the nucleon mass in nuclear medium at finite density and temperature. Using the Korea-IBS-Daegu-SKKU density functional theory, we can create models that have an identical nuclear matter equation of state but different isoscalar and isovector effective masses at zero temperature. The effect of the effective mass becomes transparent at non-zero temperatures, and it becomes more important as temperature increases. The role of the effective mass is examined thoroughly by calculating the dependence of thermodynamic variables such as free energy, internal energy, entropy, pressure and chemical potential on density, temperature and proton fraction. We find that sensitivity to the isoscalar effective mass is several times larger than that of the isovector effective mass, so the uncertainties arising from the effective mass are dominated by the isoscalar effective mass. In the analysis of the relative uncertainty, we obtain that the maximum uncertainty is less than 2% for free energy, internal energy and chemical potential, but it amounts to 20% for pressure. Entropy shows a behavior completely different from the other four variables that the uncertainty is about 40% at the saturation density and increases monotonically as density increases. The effect of the uncertainty to properties of physical systems is investigated with the proto-neutron star. It is shown that temperature depends strongly on the effective mass at a given density, and substantial swelling of the radius occurs due to the finite temperature. The equation of state is stiffer with smaller isoscalar effective mass, so the effect of the effective mass appears clearly in the mass–radius relation of the proto-neutron star, where a larger radius corresponds to a smaller effective mass. Full article

The success of the Primitivo variety underscores the critical need for the managing of clone genetic conservation, utilization, and improvement. By combining genomic and environmental data, breeders can better predict the performance of varieties, thereby improving breeding efficiency and enabling more targeted development of high-quality grapevine cultivars. In this study, 35 Primitivo clones were analysed, including selected and certified clones that have been propagated over several years in Apulia. Genetic variability among the Primitivo clones was assessed through genotyping by sequencing. Using 38,387 filtered SNPs, pairwise identity-by-state (IBS) analysis demonstrated the uniqueness of the 35 clones (IBS < 0.75), indicating a high degree of variability among the samples. Genetic diversity analysis revealed three primary groups, which were differentiated based on geographic origin. The clones from Gioia del Colle were grouped into two distinct clusters, which aligns with the observed variation in grape-related traits. The fixation index (F_ST > 0.50) identified numerous loci putatively associated with stress responses and developmental traits, including genes involved in key plant biological processes, stress response regulation, and adaptation to environmental conditions such as glutamate receptors, auxin, and ethylene signalling. Full article

Background/Objectives: Infectious bronchitis (IB) is a highly infectious avian disease caused by the infectious bronchitis virus (IBV). The disease causes lesions mainly in the respiratory, reproductive, and renal systems and has a significant economic impact on the poultry industry worldwide. Methods: We discovered two unique IBV isolates (T-62: PP737794.1 and CL-61: PP783617.1) circulating in Canada and molecularly characterized them. Results: The phylogenetic analysis revealed that the IBV isolates belong to genotype I and fall between lineages 25 and 7. Further analysis of the T-62 IBV isolate indicated that it is a potential recombinant of the Iowa state isolate (IA1162/2020-MW) and that the CL-61 strain of the IBV is also a recombinant IBV with the Connecticut (Conn) vaccine strain as its major parent. The S1 glycoprotein of the CL-61 and T-62 strains of the IBV had 85.7% and 73.2% amino acid (aa) identities respectively compared to the Conn vaccine strain. There were 67 and 129 aa substitutions among the S1 glycoprotein of the CL-61 and T-62 strains of the IBV compared to the Conn vaccine, respectively. Importantly, two and nineteen of these aa variations were in hypervariable regions 1 (HVR1) and HVR3. Finally, the two IBV isolates possessed a higher affinity for the sialic acid ligand compared to the DMV/1639 and Mass/SES IBV strains. Conclusions: Genetic recombination in the IBV results in the continual emergence of new variants, posing challenges for the poultry industry. As indicated by our analyses, live attenuated vaccine strains play a role in the genetic recombination of the IBV, resulting in the emergence of variants. Full article

With the rapid development of the Internet of Things (IoT), ensuring secure communication between devices has become a crucial challenge. This paper proposes a novel secure communication solution by extracting wireless channel state information (CSI) features from IoT devices to generate a device identity. Due to the instability of the wireless channel, the CSI features are fuzzy and time-varying; thus, we a employ locally sensitive hashing (LSH) algorithm to ensure the stability of the generated identity in a dynamically changing wireless channel environment. Furthermore, zero-knowledge proofs are utilized to guarantee the authenticity and effectiveness of the generated identity. Finally, the identity generated using the aforementioned approach is integrated into an IBE communication scheme, which involves the fuzzy extraction of channel state information from IoT devices, stable identity extraction for fuzzy IoT devices using LSH, and the use of zero-knowledge proofs to ensure the authenticity of the generated identity. This identity is then employed as the identity information in identity-based encryption (IBE), constructing the device’s public key for achieving confidential communication between devices. Full article

The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analysis certified that they belong to the same population. The outer point of the breed demarcation was a single Hungarian Wire-haired Vizsla (HWV) individual, which was the closest animal genetically to the HSV population in the PCA analysis. Three programs were used for the breed assignment calculations, including the widely used GeneClass2.0 software and two additional approaches developed here: the ‘PCA-distance’ and ‘IBS-central’ methods. Both new methods calculate a single number that represents how closely a dog fits into the actual reference population. The former approach calculates this number based on the PCA distances from the median of HSV animals. The latter calculates it from identity by state (IBS) data, measuring the distance from a central animal that is the best representative of the breed. Having no mixed-breed dogs with known HSV genome proportion, admixture animals were simulated by using data of HSV and HWV individuals to calibrate the inclusion/exclusion probabilities for the assignment. The numbers generated from these relatively simple calculations can be used by breeders and clubs to keep their populations under genetic supervision. Full article

Durian (Durio zibethinus L.) is a crop of economic and health importance globally. Efforts are being made to revamp China’s only successful commercial-scale durian plantations in Hainan; however, their genetic base is unknown. Therefore, the present study was undertaken to assess the genetic base and population structure of 32 genotypes in durian plantation sites in Hainan, China, and develop simple sequence repeat (SSR) markers by whole genome sequencing through restriction site-associated DNA sequencing technology to facilitate germplasm conservation and breeding. The results from identity by state (IBS), phylogenetic tree, population structure, and principal component analysis grouped the 32 genotypes into two clusters/sub-populations. Based on IBS, genotypes in Cluster I are largely duplicated genotypes; however, results from the model-based population structure demonstrated that most of the genotypes in Sub-population II shared a common genetic background with those in Sub-population I/Cluster I. The results revealed that the core durian collection in the plantation sites in Hainan include D24, D101, MSW, JH, D163, HFH, and NLX-5. In addition, we developed a total of 79,178 SSR markers with varied lengths and amplicon sizes. The genetic diversity and population structure reported in this study will be useful for durian conservation and utilization. In addition, the discovered and developed SSR markers will lay the foundation for molecular breeding via marker-assisted selection, quantitative trait loci mapping, and candidate gene discovery and validation. Full article

Across the globe, wireless devices with Internet facilities such as smartphones and tablets have become essential assets for communication and entertainment alike for everyday life for millions of people, which increases the network traffic and the demand for low-latency communication networks. The fourth-generation (4G)/long-term evolution (LTE)/ fifth-generation (5G) communication technology offers higher bandwidth and low latency services, but resource utilization and resiliency cannot be achieved, as transmission control protocol (TCP) is the most common choice for most of the state-of-art applications for the transport layer. An extension of TCP—multipath TCP (MPTCP)—offers higher bandwidth, resiliency, and stable connectivity by offering bandwidth aggregation and smooth handover among multiple paths. However, MPTCP uses multiple disjointed paths for communication to offer multiple benefits. A breach in the security of one of the paths may have a negative effect on the overall performance, fault-tolerance, robustness, and quality of service (QoS). In this paper, the research focuses on how MPTCP options such as MP_CAPABLE, ADD_ADDR, etc., can be used to exploit the vulnerabilities to launch various attacks such as session hijacking, traffic diversion, etc., to compromise the availability, confidentiality, and integrity of the data and network. The probable security solutions for securing MPTCP connections are analyzed, and the secure key exchange model for MPTCP (SKEXMTCP) based on identity-based encryption (IBE) is proposed and implemented. The parameters exchanged during the initial handshake are encrypted using IBE to prevent off-path attacks by removing the requirement for key exchange before communication establishment by allowing the use of arbitrary strings as a public key for encryption. The experiments were performed with IBE and an elliptic curve cryptosystem (ECC), which show that IBE performs better, as it does not need to generate keys while applying encryption. The experimental evaluation of SKEXMTCP in terms of security and performance is carried out and compared with existing solutions. Full article

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies. Full article

To prevent eavesdropping and tampering, network security protocols take advantage of asymmetric ciphers to establish session-specific shared keys with which further communication is encrypted using symmetric ciphers. Commonly used asymmetric algorithms include public key encryption, key exchange, and identity-based encryption (IBE). However, network security protocols based on classic identity-based encryption schemes do not have perfect forward secrecy. To solve this problem, we construct the first quantum IBE (QIBE) scheme based on the learning with errors (LWE) problem, which is also the first cryptographic scheme that applies the LWE problem to quantum encryption. We prove that our scheme is fully secure under the random oracle model and highlight the following advantages: (1) Network security protocols with our QIBE scheme provide perfect forward secrecy. The ciphertext is transmitted in the form of a quantum state unknown to the adversary and cannot be copied and stored. Thus, in network security protocols based on QIBE construction, the adversary does not have any previous quantum ciphertext to decrypt for obtaining the previous session key, even if the private identity key is threatened. (2) Classic key generation centre (KGC) systems can still be used in the QIBE scheme to generate and distribute private identity keys, reducing the cost when implementing this scheme. The classic KGC systems can be used because the master public and secret keys of our scheme are both in the form of classic bits. Finally, we present quantum circuits to implement this QIBE scheme and analyse its required quantum resources for given numbers of qubits, Hadamard gates, phase gates, T gates, and CNOT (controlled-NOT) gates. One of our main findings is that the quantum resources required by our scheme increase linearly with the number of plaintext bits to be encrypted. Full article

Traditional tree improvement is cumbersome and costly. Our main objective was to assess the extent to which genomic data can currently accelerate and improve decision making in this field. We used diameter at breast height (DBH) and wood density (WD) data for 4430 tree genotypes and single-nucleotide polymorphism (SNP) data for 2446 tree genotypes. Pedigree reconstruction was performed using a combination of maximum likelihood parentage assignment and matching based on identity-by-state (IBS) similarity. In addition, we used best linear unbiased prediction (BLUP) methods to predict phenotypes using SNP markers (GBLUP), recorded pedigree information (ABLUP), and single-step “blended” BLUP (HBLUP) combining SNP and pedigree information. We substantially improved the accuracy of pedigree records, resolving the inconsistent parental information of 506 tree genotypes. This led to substantially increased predictive ability (i.e., by up to 87%) in HBLUP analyses compared to a baseline from ABLUP. Genomic prediction was possible across populations and within previously untested families with moderately large training populations (N = 800–1200 tree genotypes) and using as few as 2000–5000 SNP markers. HBLUP was generally more effective than traditional ABLUP approaches, particularly after dealing appropriately with pedigree uncertainties. Our study provides evidence that genome-wide marker data can significantly enhance tree improvement. The operational implementation of genomic selection has started in radiata pine breeding in New Zealand, but further reductions in DNA extraction and genotyping costs may be required to realise the full potential of this approach. Full article