Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan.

Geographical wildlife patterns reflect historical range expansion and connectivity and provide insights into wildlife population management. In our large-scale phylogeographic population analysis of wild boars (Sus scrofa leucomystax) in Japan, we identified 15 clusters using 29 microsatellite markers, each structured within a range of approximately 200 km. This suggests that evolution was essentially driven by isolation by distance, and that the range of gene flow was limited. One cluster contained subpopulations located approximately 900 km apart, indicating the occurrence of past anthropogenic introductions. Moreover, we estimated effective migration to visualize the geographic genetic population diversity. This analysis identified six potential barriers, one of which involved large plains and mountainous areas in the Kanto region of eastern Japan. This barrier likely persisted in the two eastern clusters for an extended period, restricting migration to the neighboring areas. Overall, our study sheds light on the demographic history of wild boar in Japan, provides evidence of past anthropogenic introductions from distant areas, and highlights the importance of geographic barriers in shaping genetic diversity and population dynamics. This knowledge will be beneficial for forming informed wildlife management strategies toward the conservation of genetic integrity and ecological balance of wild boar populations in Japan.

Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle.

We collected 3180 records of oleic acid (C18:1) and monounsaturated fatty acid (MUFA) measured using gas chromatography (GC) and 6960 records of C18:1 and MUFA measured using near-infrared spectroscopy (NIRS) in intermuscular fat samples of Japanese Black cattle. We compared genomic prediction performance for four linear models (genomic best linear unbiased prediction [GBLUP], kinship-adjusted multiple loci [KAML], BayesC, and BayesLASSO) and five machine learning models (Gaussian kernel [GK], deep kernel [DK], random forest [RF], extreme gradient boost [XGB], and convolutional neural network [CNN]). For GC-based C18:1 and MUFA, KAML showed the highest accuracies, followed by BayesC, XGB, DK, GK, and BayesLASSO, with more than 6% gain of accuracy by KAML over GBLUP. Meanwhile, DK had the highest prediction accuracy for NIRS-based C18:1 and MUFA, but the difference in accuracies between DK and KAML was slight. For all traits, accuracies of RF and CNN were lower than those of GBLUP. The KAML extends GBLUP methods, of which marker effects are weighted, and involves only additive genetic effects; whereas machine learning methods capture non-additive genetic effects. Thus, KAML is the most suitable method for breeding of fatty acid composition in Japanese Black cattle.

Population structure of Vietnamese pigs using mitochondrial DNA.

The D-loop region on mitochondrial DNA (mtDNA) is frequently used for analyses of maternal lineages within domestic animal species. There are many native pig breeds in Vietnam, but their origins remain unclear. This study investigated maternal lineages using the D-loop region on mtDNA of 260 samples collected from native pigs in 20 provinces across Vietnam. The D-loop region of all samples was amplified and sequenced. We obtained 713 bp sequences of the D-loop region for each sample excluding the repeat region, and variants on this region were used to construct a phylogenetic tree. We detected 50 haplotypes from Vietnamese native pigs, with 27 novel haplotypes. Phylogenetic tree analysis showed two haplotype groups: one for the MTSEA group, frequently found in domestic pigs in the mountainous areas of Cambodia and Laos; and the D2 group, found in pigs originating from Chinese pigs. No European haplotype was found. Haplotypes in northeast Vietnam comprised only haplotypes of the D2 group, whereas in areas from the northwest mountains to the south, we found haplotypes belonging to both the D2 and MTSEA groups. This study suggested that both origins contributed to maternal lineages of current populations of Vietnamese native pigs.

Safety and Efficacy of Prasugrel Administration in Emergent Endovascular Treatment for Intracranial Atherosclerotic Disease.

Objective: Intracranial atherosclerosis disease (ICAD) is one of the most common causes of acute ischemic stroke. In endovascular treatment (EVT) for acute large vessel occlusion stroke-related ICAD, reocclusion of the recanalized artery due to in situ thrombosis is problematic. In this study, the safety and efficacy of prasugrel administration to avoid reocclusion of emergent EVT for ICAD was investigated. Methods: All consecutive emergent EVTs for ICAD between September 2019 and December 2022 were included in this study. The procedures were divided into two groups as receiving periprocedural prasugrel (PSG group) or not (non-PSG group). Target vessel patency on follow-up, postprocedural intracranial hemorrhage (ICH), and clinical outcome were compared between PSG and non-PSG groups. Results: A total of 27 procedures were included in this analysis. Nineteen target vessels were patent on follow-up and eight were non-patent. Fifteen patients received prasugrel (18.75 mg: 11 cases, 11.25 mg: 4 cases), and twelve patients did not receive prasugrel. The target vessel patency rate was better in the PSG group vs. non-PSG group (100% vs. 33.3%, respectively; p = 0.0002). The postprocedural ICH rate was not different between the groups (PSG: 40.0% vs. non-PSG: 25.0%; p = 0.68), and all ICHs were asymptomatic. Good clinical outcome (modified Rankin Scale score of 0 to 3 at discharge) was more frequent in the PSG group than that in the non-PSG group (66.7% vs. 16.7%, respectively; p = 0.019). Conclusion: Prasugrel administration was significantly associated with target vessel patency and good clinical outcome after emergent EVT for ICAD without increasing the symptomatic ICH rate. Prasugrel administration might be safe and effective to avoid reocclusion during and after emergent EVT for ICAD.

Evaluating the performance of genomic prediction accounting for effects of single nucleotide polymorphism markers in reproductive traits of Japanese Black cattle.

We examined the prediction accuracies of genomic best linear unbiased prediction (GBLUP), various weighted GBLUP according to the degrees of marker effects (WGBLUP) and machine learning (ML) methods, and compared them with traditional BLUP for age at first calving (AFC), calving difficulty (CD), and gestation length in Japanese Black cattle. For WGBLUP, firstly, BayesC and FarmCPU were used to estimate marker effects. Then, we constructed three weighted genomic relationship matrices from information of estimated marker effects in the first step: absolute value of the estimated marker-effect WGBLUP, estimated marker-variance WGBLUP, and genomic-feature WGBLUP. For ML, we applied Gaussian kernel, random forest, extreme gradient boost, and support vector regression. We collected a total of 2583 animals having both phenotypic records and genotypes with 30,105 markers and 16,406 pedigree records. For AFC, prediction accuracies of WGBLUP methods using FarmCPU exceeded BLUP by 25.7%-39.5%. For CD, estimated marker-variance WGBLUP using BayesC achieved the highest prediction accuracy. Among ML methods, extreme gradient boost, support vector regression, and Gaussian kernel increased prediction accuracies by 28.4%, 19.0%, and 36.4% for AFC, CD, and gestation length compared with BLUP, respectively. Thus, prediction performance could be improved using suitable WGBLUP and ML methods according to target reproductive traits for the population used.

Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle.

BACKGROUND: Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and depression. Recently, many measures have been used for genome-based inbreeding coefficients; however, with no consensus on which is the most appropriate. Therefore, we compared the pedigree- ([Formula: see text]) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ([Formula: see text]), correlation between uniting gametes ([Formula: see text]), the observed vs expected number of homozygous genotypes ([Formula: see text]), runs of homozygosity (ROH) segments ([Formula: see text]) and heterozygosity by descent segments ([Formula: see text]). We quantified inbreeding depression from estimating regression coefficients of inbreeding coefficients on three reproductive traits: age at first calving (AFC), calving difficulty (CD) and gestation length (GL) in Japanese Black cattle. RESULTS: The highest correlations with [Formula: see text] were for [Formula: see text] (0.86) and [Formula: see text] (0.85) whereas [Formula: see text] and [Formula: see text] provided weak correlations with [Formula: see text], with range 0.33-0.55. Except for [Formula: see text] and [Formula: see text], there were strong correlations among genome-based inbreeding coefficients ([Formula: see text] 0.94). The estimates of regression coefficients of inbreeding depression for [Formula: see text] was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but [Formula: see text] had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than [Formula: see text]. In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for [Formula: see text] had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, [Formula: see text] provided significant effects at chromosomal level in four chromosomes for AFC, three chromosomes for CD, and two chromosomes for GL. In addition, similar results were obtained for [Formula: see text]. CONCLUSIONS: Genome-based inbreeding coefficients can capture more phenotypic variation than [Formula: see text]. In particular, [Formula: see text] and [Formula: see text] can be considered good estimators for quantifying inbreeding level and identifying inbreeding depression at the chromosome level. These findings might improve the quantification of inbreeding and breeding programs using genome-based inbreeding coefficients.

Expression and differential posttranscriptional regulation of the elongation factor 1 alpha 1 gene in endometrial caruncle and intercaruncle of Japanese Black cattle at early and mid-gestation stages.

The elongation factor 1 alpha 1 (EEF1A1), an isoform of EEF1A, is one of the most abundant cytoplasmic proteins and an important component of the translational machinery. We investigated the relative expression, alternative polyadenylation (APA), and changes in poly(A) tail length of EEF1A1 mRNA in the endometrial caruncle (CAR) and intercaruncle (ICAR) at early and mid-gestation in Japanese Black cattle. The relative EEF1A1 mRNA expression levels in the CAR were the highest on Gestation day 20 and were significantly decreased at mid-gestation. The expression levels in the ICAR were significantly higher than those in the CAR, and the gestation stage had no significant impact. Four different EEF1A1 transcripts with distinct 3' untranslated regions (UTRs) (proximal and distal types) and poly(A) tails (medium and short types) of different lengths were identified. The EEF1A1 mRNAs with distal 3' UTR and medium-length poly(A) tails were specific from the CAR of uterus horn at early gestation. RNA-sequencing data analyses revealed that the HSF1, MZF1, E47, SRF, GATA2, GATA3, GATA6, HNF-3 beta (FOXA2), CPSF1, and Ataxin-2 genes might affect the EEF1A1 gene expression or poly(A) length.

Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome.

The Vietnamese native pig (VnP)-a porcine breed with a small body-has proven suitable as a biomedical animal model. Here, we demonstrate that, compared to other breeds, VnPs have fewer copies of porcine endogenous retroviruses (PERVs), which pose a risk for xenotransplantation of pig organs to humans. More specifically, we sought to characterize non-reference PERVs (nrPERVs) that were previously unidentified in the reference genome. To this end, we used whole-genome sequencing data to identify nrPERV loci with long terminal repeat (LTR) sequences in VnPs. RetroSeq was used to estimate nrPERV loci based on the most current porcine reference genome (Sscrofa11.1). LTRs were detected using de novo sequencing read assembly near the loci containing the target site duplication sequences in the inferred regions. A total of 21 non-reference LTR loci were identified and separated into two subtypes based on phylogenetic analysis. Moreover, PERVs within the detected LTR loci were identified, the presence of which was confirmed using conventional PCR and Sanger sequencing. These novel loci represent previously unknown PERVs as they have not been identified in the porcine reference genome. Thus, our RetroSeq method accurately detects novel PERV loci, and can be applied for development of a useful biomedical model.

Hamiltonian Monte Carlo method for estimating variance components.

A Hamiltonian Monte Carlo algorithm is a Markov chain Monte Carlo method, and the method has a potential to improve estimating parameters effectively. Hamiltonian Monte Carlo is based on Hamiltonian dynamics, and it follows Hamilton's equations, which are expressed as two differential equations. In the sampling process of Hamiltonian Monte Carlo, a numerical integration method called leapfrog integration is used to approximately solve Hamilton's equations, and the integration is required to set the number of discrete time steps and the integration stepsize. These two parameters require some amount of tuning and calibration for effective sampling. In this study, we applied the Hamiltonian Monte Carlo method to animal breeding data and identified the optimal tunings of leapfrog integration for normal and inverse chi-square distributions. Then, using real pig data, we revealed the properties of the Hamiltonian Monte Carlo method with the optimal tuning by applying models including variance explained by pedigree information or genomic information. Compared with the Gibbs sampling method, the Hamiltonian Monte Carlo method had superior performance in both models. We have provided the source codes of this method written in the Fortran language at https://github.com/A-ARAKAWA/HMC.

Newly Identified Hemodynamic Parameter to Predict Thin-Walled Regions of Unruptured Cerebral Aneurysms Using Computational Fluid Dynamics Analysis.

BACKGROUND: The thin-walled regions (TIWRs) of intracranial aneurysms have a high risk of rupture during surgical manipulation. They have been reported to be predicted by wall shear stress and pressure (PS) based on computational fluid dynamics analysis, although this remains controversial. In this study, we investigated whether the oscillatory shear index (OSI) can predict TIWRs. METHODS: Twenty-five unruptured aneurysms were retrospectively analyzed; the position and orientation of the computational fluid dynamics color maps were adjusted to match the intraoperative micrographs. The red area on the aneurysm wall was defined as TIWR, and if most of the regions on the color map corresponding to TIWR were OSI low (lower quartile range), time-averaged wall shear stress (TAWSS) high, or PS high (upper quartile range), each region was defined as a matched region and divided by the total number of TIWRs to calculate the match rate. In addition, the mean values of OSI, TAWSS, and PS corresponding to TIWRs were quantitatively compared with those in adjacent thick-walled regions. RESULTS: Among 27 TIWRs of 25 aneurysms, 23, 10, and 14 regions had low OSI, high TAWSS, and high PS regions (match rate: 85.2%, 37.0%, and 51.9%), respectively. Receiver operating characteristic curve analysis demonstrated that OSI was the most effective hemodynamic parameter (area under the curve, 0.881), followed by TAWSS (0.798). Multivariate analysis showed that OSI was a significant independent predictor of TIWRs (odds ratio, 18.30 [95% CI, 3.2800-102.00], P < 0.001). CONCLUSIONS: OSI may be a unique predictor for TIWRs. Low OSI strongly corresponds with TIWRs of intracranial aneurysms.

Effect of a genetic polymorphism in SREBP1 on fatty acid composition and related gene expression in subcutaneous fat tissue of beef cattle breeds.

Sterol regulatory element-binding factor 1 (SREBP1) plays an important role in the lipogenesis which affects fatty acid (FA) composition in backfat and consequently influences beef nutritional quality. This study analyzed the association of 84 bp-indel, both short (S) and long (L) alleles in intron 5 of SREBP1, with FA composition and gene expression of SREBP1 in backfat of northern Spanish beef breeds (Pirenaica, Salers and Holstein-Friesian). Phylogenetic analysis suggests that 84 bp-indel of ruminants is a highly conserved region compared with those in the full-length sequence of intron 5 or mRNA of SREBP1 among species. Overall, higher content of polyunsaturated FAs was observed in SL genotype compared to LL genotype of 84 bp-Indel (p < .05). In particular, in Pirenaica, SL genotype was associated with a higher content of stearic (18:0), α-linolenic (18:3n-3) acid, and total n-3 content (p < .05). However, the gene expression of SREBP1 did not differ among genotypes of 84 bp-Indel (p > .05).

Anatomical variation of the internal carotid artery and its implication to the endoscopic endonasal translacerum approach.

BACKGROUND: The endoscopic endonasal trans-lacerum approach (EETLA) is useful in handling skull base tumors around inferior petrous apex (IPA); however, its surgical corridor is exclusively a triangular space (supra-eustachian triangle [SET]), between the internal carotid artery (ICA) and eustachian tube. METHODS: We investigated correlation between SET size and extent of resection around the IPA (lateral extent of resection [EOR]) through a retrospective analysis of 15 surgeries using EETLA. RESULTS: Of 15 cases (9 chordomas, 4 chondrosarcomas, and 2 meningiomas), 20 sides of IPA were affected by the tumor. When being restricted to sides with severe lateral tumor extension beyond the midpoint of petrous ICA (10 sides), the SET size was significantly broader in the group with lateral EOR of ≥90% (p value = 0.019). CONCLUSIONS: The SET size was a powerful index of tumor resectability in EETLA, especially in cases with severe tumor extension. The individual anatomical variations should be considered when determining EETLA application.

Acute Occlusion of the Ventriculoperitoneal Shunt Due to Factor XIII Deficiency-related Postoperative Hemorrhage: A Case Report.

Coagulation factor XIII (F13) deficiency has been known to be a rare disease with estimated one per two million and one of the possible reasons of postoperative hemorrhage; however, it still remains unpenetrated to physicians. We report a case of acute ventriculoperitoneal (VP) shunt dysfunction due to delayed intraventricular hemorrhage, which could be because of F13 deficiency. The patient was a 48-year-old man with a history of post-meningitis hydrocephalus followed by VP shunt placement. He was found unconscious and transferred to our hospital. A brain CT scan demonstrated shunt malfunction, and he underwent emergency shunt revision. The postoperative course was uneventful except for unexpected neck bruises and continuous minor bleeding from the surgical wound. Three days after surgery, he suddenly became comatose and a CT scan revealed the recurrence of hydrocephalus with newly identified small volume of intraventricular hemorrhage. Emergency shunt revision was performed again. The shunt valve was filled with a hematoma and bloody cerebrospinal fluid was drained from the ventricle. Postoperative blood sample examination demonstrated no abnormal findings but a decreased level of F13 activity, which was thought to be a possible cause of postoperative hemorrhage and the shunt valve hematoma. F13 deficiency causes delayed intracranial hemorrhage 24-48 h after neurological surgery. It can only be diagnosed by checking F13 activity with suspicion. If diagnosed accurately beforehand, unexpected postoperative bleeding can be preventable with proper treatment, such as F13 concentrate and cryoprecipitate. The actual number of the patient with F13 deficiency may be more than estimated ever.

[Sellar and Parasellar Inflammatory Lesions with Impaired Visual Function:Clinical Features and Endoscopic Surgical Outcomes of Six Cases].

Accurate diagnosis and treatment of sellar and parasellar inflammatory lesions is difficult. We report six patients with sellar and parasellar inflammatory lesions and impaired visual function, who underwent endonasal endoscopic surgery. These patients included one with aspergillosis, one with hypertrophic pachymeningitis, one patient with abscess, and three with idiopathic granulomatous lesions. Following surgery and medication, visual function improved in patients with aspergillosis, hypertrophic pachymeningitis, and abscess. In patients with idiopathic granulomatous inflammation, visual function improved in one out of three patients. The treatment outcome for sellar and parasellar inflammatory lesions with impaired visual function depends on the surgery as well as on the reaction to postoperative medication. In the present study, the functional prognosis of patients with idiopathic granulomatous lesions was relatively poor when compared with that of patients with other inflammatory lesions.

Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes.

Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10-25 and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest FST in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest FST markers is proposed for a confident parentage analysis and high traceability.

Differential Metabolomics Profiles Identified by CE-TOFMS between High and Low Intramuscular Fat Amount in Fattening Pigs.

The amount of intramuscular fat (IMF) present in the loin eye area is one of the most important characteristics of high-quality pork. IMF measurements are currently impractical without a labor-intensive process. Metabolomic profiling could be used as an IMF indicator to avoid this process; however, no studies have investigated their use during the fattening period of pigs. This study examined the metabolite profiles in the plasma of two groups of pigs derived from the same Duroc genetic line and fed the same diet. Five plasma samples were collected from each individual the day before slaughter. Capillary electrophoresis-time of flight mass spectrometry (CE-TOFMS) was used to analyze the purified plasma from each sample. Principle component analysis (PCA) and partial least squares (PLS) were used to find the semi-quantitative values of the compounds. The results indicate that branched-chain amino acids are significantly associated with high IMF content, while amino acids are associated with low IMF content. These differences were validated using the quantification analyses by high-performance liquid chromatograph, which supported our results. These results suggest that the concentration of branched-chain amino acids in plasma could be an indicative biomarker for the IMF content in the loin eye area.

The phenotypic characteristics and relational database for Vietnamese native pig populations.

Although there are a number of Vietnamese native pig (VnP) populations, some are on the verge of extinction, and therefore adequate management and conservation are necessary. In this study, we conducted a field survey of VnP populations and analyzed interrelationships among their characteristics. We also established a relational database for management of field data on these populations. For data collection, we conducted interviews with farmers and visual inspection of 32 VnP populations in 22 provinces of Vietnam, as well as taking photographs of individual animals. Data on the characteristics of VnP populations were subjected to multiple correspondence analysis (MCA). For establishment of the database, normalization and table partitioning were performed to eliminate redundancy and ensure consistency of the collected data items. Passport data, characteristics data, and image data were collected from a total of 1,918 VnPs and entered as a normalized table. Upon MCA, most of the populations were not separated from each other, but the Mong Cai, O Lam, and Chu Prong populations were separated from the other populations. Thus, we have constructed a relational database from comprehensive information on the characteristics of VnP populations.

Submucosal Inferior Turbinectomy to Widen the Surgical Corridor for Endoscopic Endonasal Skull Base Surgery.

The nasal cavity is the exclusive surgical corridor for endoscopic endonasal surgery; however, it is sometimes too narrow to allow extensive surgical maneuvering. Here we show the technique of submucosal inferior turbinectomy (SIT) to widen this surgical corridor. Its effectiveness is evaluated quantitatively by comparing pre- and intraoperative magnetic resonance images. Between March 2015 and October 2018, we performed endoscopic endonasal resection of 57 skull base tumors with 3T intraoperative magnetic resonance imaging (iMRI). Among these resections, cases with previous endonasal surgery and cases for which the iMRI did not cover the entire nasal cavity were excluded. Finally, six cases with and 19 cases without SIT were included in the subsequent retrospective analysis. We measured the dimensions of the narrowest area in inferior nasal cavity on pre- and intraoperative coronal plane gadolinium (Gd)-enhanced T1-weighted MR images using dedicated software, and compared them. The incidence rates of postoperative nasal complaints at outpatient clinics were also compared. Considerable widening of the inferior nasal cavity could be achieved with the SIT, which was statistically significant compared with those without the SIT (111.1 ± 56.5% vs. 39.4 ± 59.4%, respectively; P = 0.0093). In terms of the incidence rate of postoperative nasal complaints at 6 months, there was no statistical difference between the groups (33.3% vs. 15.8%, respectively; P = 0.35). SIT is effective for widening the surgical corridor while keeping nasal function and is especially helpful for lower clivus and laterally extended skull base lesions.