Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

Background CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. Results Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. Conclusion For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments

Correction to: Population diferentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

Following publication of the original article [1], the authors reported that the following missing authors from the authorship list: • Endashaw Terefe • Gurja Belay • Abdulfatai Tijjani • Jian-Lin Han • Olivier Hanotte The corrected authorship list and the updated ‘Authors’ contributions’ and ‘Acknowledgements’ declarations are provided in this Correction article. The original article [1] has been updated

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

BackgroundCNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.ResultsHere, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs.ConclusionFor some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments

The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750–1,050 yr ago, which has shaped the genome of today’s cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism

Medial Temporal Atrophy and Memory Dysfunction in Poststroke Cognitive Impairment-No Dementia

Background and Purpose It was recently reported that the prevalence of poststroke memory dysfunction might be higher than previously thought. Stroke may exist concomitantly with underlying Alzheimer's disease (AD), and so we determined whether post-stroke memory dysfunction indicates manifestation of underlying subclinical AD. Methods Of 1201 patients in a prospective cognitive assessment database, we enrolled subjects with poststroke amnestic vascular cognitive impairment-no dementia (aVCIND; n=48), poststroke nonamnestic vascular cognitive impairment-no dementia (naVCIND; n=50), and nonstroke amnestic mild cognitive impairment (aMCI; n=65). All subjects had cognitive deficits, but did not meet the criteria for dementia. A standardized neuropsychological test battery and magnetic resonance imaging were performed at least 90 days after the index stroke (mean, 473 days). Visual assessment of medial temporal atrophy (MTA) was used as a measure of underlying AD pathology. Results The MTA score was significantly lower in the naVCIND group (0.64 +/- 0.85, mean +/- SD) than in the aVCIND (1.10+/-1.08) and aMCI (1.45+/-1.13; p<0.01) groups. Multivariable ordinal logistic regression analysis revealed that compared with naVCIND, aVCIND [odds ratio (OR)=2.69; 95% confidence interval (CI)=1.21-5.99] and aMCI (OR=5.20; 95% C1=2.41-11.23) were significantly associated with increasing severity of MTA. Conclusions Our findings show that compared with poststroke naVCIND, the odds of having more-severe MTA were increased for poststroke aVCIND and nonstroke aMCI. J Clio Neurol 2012;8:43-50N

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

Meta-Transformer: A Meta-Learning Framework for Scalable Automatic Modulation Classification

Recent advances in deep learning (DL) have led many contemporary automatic modulation classification (AMC) techniques to use deep networks in classifying the modulation type of incoming signals at the receiver. However, current DL-based methods face scalability challenges, particularly when encountering unseen modulations or input signals from environments not present during model training, making them less suitable for real-world applications like software-defined radio devices. In this paper, we introduce a scalable AMC scheme that provides flexibility for new modulations and adaptability to input signals with diverse configurations. We propose the Meta-Transformer, a meta-learning framework based on few-shot learning (FSL) to acquire general knowledge and a learning method for AMC tasks. This approach empowers the model to identify new unseen modulations using only a very small number of samples, eliminating the need for complete model retraining. Furthermore, we enhance the scalability of the classifier by leveraging main-sub transformer-based encoders, enabling efficient processing of input signals with diverse setups. Extensive evaluations demonstrate that the proposed AMC method outperforms existing techniques across all signal-to-noise ratios (SNRs) on RadioML2018.01A. The source code and pre-trained models are released at https://github.com/cheeseBG/meta-transformer-amc

Robust Video Stabilization Using Particle Keypoint Update and l1-Optimized Camera Path

Acquisition of stabilized video is an important issue for various type of digital cameras. This paper presents an adaptive camera path estimation method using robust feature detection to remove shaky artifacts in a video. The proposed algorithm consists of three steps: (i) robust feature detection using particle keypoints between adjacent frames; (ii) camera path estimation and smoothing; and (iii) rendering to reconstruct a stabilized video. As a result, the proposed algorithm can estimate the optimal homography by redefining important feature points in the flat region using particle keypoints. In addition, stabilized frames with less holes can be generated from the optimal, adaptive camera path that minimizes a temporal total variation (TV). The proposed video stabilization method is suitable for enhancing the visual quality for various portable cameras and can be applied to robot vision, driving assistant systems, and visual surveillance systems

Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies

Abstract This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. This is the first genome assembly of Asian taurus breed. Also, we constructed a pangenome graph of 14 B. taurus genome assemblies. The contig N50 was over 55 Mb, the scaffold N50 was over 89 Mb and a genome completeness of 95.8%, as estimated by BUSCO using the mammalian set, indicated a high-quality assembly. 48.7% of the genome comprised various repetitive elements, including DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. A total of 27,314 protein-coding genes were identified, including 25,302 proteins with inferred gene names and 2,012 unknown proteins. The pangenome graph of 14 B. taurus autosomes revealed 528.47 Mb non-reference regions in total and 61.87 Mb Hanwoo-specific regions. Our Hanwoo assembly and pangenome graph provide valuable resources for studying B. taurus populations

Effects of Cr on High-temperature Tensile Properties in High-Ni-containing Austenitic Cast Steels

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