Widespread false gene gains caused by duplication errors in genome assemblies

Abstract Background False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Annas Hummingbird, and their new counterparts of the same species generated by the Vertebrate Genomes Project, of which the Vertebrate Genomes Project pipeline attempted to eliminate false duplications through haplotype phasing and purging. These assemblies are among the first generated by the Vertebrate Genomes Project where there was a prior chromosomal level reference assembly to compare with. Results Whole genome alignments revealed that 4 to 16% of the sequences are falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These lead to overestimated gene family expansions. The main source of the false duplications is heterotype duplications, where the haplotype sequences were relatively more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source is sequencing errors. Ancient ATP nucleotide binding gene families have a higher prevalence of false duplications compared to other gene families. Although present in a smaller proportion, we observe false duplications remaining in the Vertebrate Genomes Project assemblies that can be identified and purged. Conclusions This study highlights the need for more advanced assembly methods that better separate haplotypes and sequence errors, and the need for cautious analyses on gene gains

Genetic Adaptations in Mudskipper and Tetrapod Give Insights into Their Convergent Water-to-Land Transition

Water-to-land transition has been independently evolved in multiple vertebrate lineages including the most recent common ancestor of tetrapod and multiple fish clades, and among them, mudskippers uniquely adapted to the mudflat. Even though physiological and morphological adaptation of mudskippers is thought to resemble that of the ancestral tetrapod, it is unclear if they share genome-wide evolutionary signatures. To detect potential signatures of positive selection in mudskipper and tetrapods, we analyzed 4118 singleton orthologues of terrestrial tetrapods, coelacanth, mudskipper, and fully aquatic fishes. Among positively selected genes identified in mudskipper and tetrapod lineages, genes involved in immune responses, mitochondrial oxidative phosphorylation, and kidney development were detected. On the other hand, tetrapod-specific and mudskipper-specific positively selected genes were functionally enriched for DNA repair processes, which could be associated with higher exposure to UV light. We also performed gene family analysis and discovered convergent contraction of eight gene families, including βγ-crystallin coding genes in both tetrapod and mudskipper lineages. Findings of this study suggest the similar genetic adaptation against environmental constraints between the ancient tetrapod and mudskippers for their land adaptation

Design of a Highly Efficient N-Stage Harmonic Terminated Voltage Multiplier for Wireless Power Transfer

This paper proposes a 5.8 GHz highly efficient rectifier design using harmonic termination for wireless power transfer. The diode used to convert the received RF power to DC is a non-linear device, and a harmonic component is generated, which causes performance degradation. Therefore, in this paper, we designed a band stop filter for harmonic termination and proposed the N-stage harmonic terminated voltage multiplier (N-stage HTVM). The number of stages N can be designed differently to operate with high efficiency at various input powers for the proposed rectifier. In the proposed rectifier circuit, mathematical analysis of output DC voltage, power loss of the diode, and the power conversion efficiency (PCE) were evaluated through voltage/current waveform analysis of the diode. The design method of the filter for terminating harmonics is presented. Furthermore, the change of PCE according to the increase in the number of stages was analyzed using the equivalent model of the proposed circuit and verified through measurement. The maximum PCE of one-stage HTVM was 68% when 18 dBm of input power was applied. The DC output voltage was measured to 11.6 V. When the RF input power was 25 dBm and the load was 1500 Ω, the maximum PCE of the two-stage HTVM was 71% and the maximum DC output voltage was measured as 15.8 V. The measured performance of three-stage HTVM had a PCE of 67% and DC output voltage of 19.8 V when the input power was 30 dBm

Optimal Multi-Interface Selection for Mobile Video Streaming in Efficient Battery Consumption and Data Usage

With the proliferation of high-performance, large-screen mobile devices, users’ expectations of having access to high-resolution video content in smooth network environments are steadily growing. To guarantee such stable streaming, a high cellular network bandwidth is required; yet network providers often charge high prices for even limited data plans. Moreover, the costs of smoothly streaming high-resolution videos are not merely monetary; the device’s battery life must also be accounted for. To resolve these problems, we design an optimal multi-interface selection system for streaming video over HTTP/TCP. An optimization problem including battery life and LTE data constraints is derived and then solved using binary integer programming. Additionally, the system is designed with an adoption of split-layer scalable video coding, which provides direct adaptations of video quality and prevents out-of-order packet delivery problems. The proposed system is evaluated using a prototype application in a real, iOS-based device as well as through experiments conducted in heterogeneous mobile scenarios. Results show that the system not only guarantees the highest-possible video quality, but also prevents reckless consumption of LTE data and battery life

Magnetic Heating Effect for Quarter-Wave Resonator (QWR) Superconducting Cavities

In this paper, the magnetic heating effect of the superconducting quarter-wave resonator (QWR) cavities is investigated, and the Q slopes of the superconducting cavities are measured with an increasing accelerating field. Bardeen–Cooper–Schrieffer (BCS) resistance is calculated for the zero-temperature limit. The vertical test is shown for the performance test of the QWR cavities. The parameters for the QWR cavity are presented. The Q slopes are measured as a function of an accelerating electric field at 4.2 K. The surface resistance of the superconducting cavity increases with an increasing peak magnetic field. The magnetic defects degrade the quality factor. From the magnetic degradation, we determine the magnetic moments of the superconducting cavities. All quarter-wave resonator (QWR) cryomodules are installed in the tunnel, and beam commissioning is performed successfully

Genetic Adaptations in Mudskipper and Tetrapod Give Insights into Their Convergent Water-to-Land Transition

Water-to-land transition has been independently evolved in multiple vertebrate lineages including the most recent common ancestor of tetrapod and multiple fish clades, and among them, mudskippers uniquely adapted to the mudflat. Even though physiological and morphological adaptation of mudskippers is thought to resemble that of the ancestral tetrapod, it is unclear if they share genome-wide evolutionary signatures. To detect potential signatures of positive selection in mudskipper and tetrapods, we analyzed 4118 singleton orthologues of terrestrial tetrapods, coelacanth, mudskipper, and fully aquatic fishes. Among positively selected genes identified in mudskipper and tetrapod lineages, genes involved in immune responses, mitochondrial oxidative phosphorylation, and kidney development were detected. On the other hand, tetrapod-specific and mudskipper-specific positively selected genes were functionally enriched for DNA repair processes, which could be associated with higher exposure to UV light. We also performed gene family analysis and discovered convergent contraction of eight gene families, including βγ-crystallin coding genes in both tetrapod and mudskipper lineages. Findings of this study suggest the similar genetic adaptation against environmental constraints between the ancient tetrapod and mudskippers for their land adaptation

Human Activity Recognition via Temporal Fusion Contrastive Learning

With recent advancements in wearable devices and the Internet of Things (IoT), human activity recognition (HAR) has attracted increasing interest in the wearable technology market. However, for sensor-based HAR, collecting sufficient labeled data for deep neural network learning is difficult because experts must find visually recognizable patterns in time-series data. In addition, collecting data is difficult due to privacy issues. To overcome these limitations, self-supervised learning (SSL)-based HAR methods have recently been proposed; these can learn representations without using labeled data. However, such methods only utilize sensor data and do not include the sensor wearer&#x2019;s biometric information. A learning method that excludes biometric information can identify typical movement patterns but cannot learn customized movement patterns effectively. Thus, in this paper, we proposed the Temporal Fusion Contrastive Learning (TFCL) method, which considers a sensor wearer&#x2019;s biometric information while training. Experimental results demonstrate that, when fine-tuned with biometric information, the proposed TFCL method obtained the highest F1 score of 0.9791 and 0.7433 on the DLR and MobiAct datasets, respectively. Furthermore, the results obtained when the proposed TFCL method was used to learn the representation and then applied to the downstream task were similar to or better than those obtained using supervised learning from scratch. These results indicate that representations can be learned effectively through TFCL. The experimental code can be found on GitHub at https://github.com/IKKIM00/temporal-fusion-contrastive-learning</uri

Association between metabolic syndrome and blepharoptosis in the Korean adults: the Korea National Health and Nutrition Examination Survey 2010–2012

Background : : Metabolic syndrome (MetS) is a complex disorder featuring chronic inflammation characterized by abdominal obesity, hyperglycemia, hypertension, and dyslipidemia. Recent studies have documented that MetS is associated with various diseases, including ocular disorders. Objective: This cross-sectional study is based on data from the fifth Korea National Health and Nutrition Examination Surveys. We examined the association between MetS and its components with blepharoptosis in Korean adults aged 19 years or older. Methods : : MetS was defined using the criteria proposed by the American Heart Association and the National Heart, Lung, and Blood Institute together with the International Diabetes Federation in 2009. Blepharoptosis was defined as the marginal reflex distance 1 of <2 mm. Results : : The prevalence of blepharoptosis was 11.5%. As the number of MetS components increased, the prevalence of blepharoptosis also increased. After being controlled for various confounders, MetS was significantly associated with blepharoptosis (adjusted odds ratio [OR], 1.316; 95% confidence interval [CI], 1.133-1.529). In addition, blepharoptosis was associated with increased waist circumference, hypertension, and elevated triglyceride (adjusted OR, 95% CI; 1.281 [1.047-1.567], 1.165 [1.014-1.339], and 1.174 [1.013-1.36], respectively). Conclusion : : Consequently, MetS and its components were associated with blepharoptosis in Korean adults. Screening for blepharoptosis is warranted for patients with MetS