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Motivation Long-read phasing has been used for reconstructing diploid genomes, improving variant calling and resolving microbial strains in metagenomics. However, the phasing blocks of existing methods are broken by large Structural Variations (SVs), and the efficiency is unsatisfactory for population-scale phasing. Results This article presents a novel algorithm, LongPhase, which can simultaneously phase single nucleotide polymorphisms (SNPs) and SVs of a human genome in 10–20 min, 10× faster than the state-of-the-art WhatsHap, HapCUT2 and Margin. In particular, co-phasing SNPs and SVs produces much larger haplotype blocks (N50 = 25 Mbp) than those of existing methods (N50 = 10–15 Mbp). We show that LongPhase combined with Nanopore ultra-long reads is a cost-effective and highly contiguous solution, which can produce between one and 26 blocks per chromosome arm without the need for additional trios, chromosome-conformation and strand-seq data. Availabilityand implementation LongPhase is freely available at https://github.com/twolinin/LongPhase/. Supplementary information Supplementary data are available at Bioinformatics online.

Objective Shewanella algae is a zoonotic marine bacterium that causes a variety of infections in immunocompromised patients or those who have been exposed to seawater. The development of trimethoprim/sulfamethoxazole (TMP/SMX) resistance in S. algae are found in human and environment isolates during the past ten years, and thus the treatment options are decreasing. Methodology In the study, we conduct a comparative genomic study to identify the resistant mechanism of TMP/SMX-resistance in S. algae. Results We found the resistance of TMP/SMX in S. algae is associated with the existence of sul1 and dfrA12 within the class 1 integron. The gene cassette dfra12-aadA2-qacEΔ1/sul1 within the class 1 integron is highly conserved. In addition, the class 1 integron and encapsulated sul1 are significantly enriched in Enterobacteriaceae in NCBI and UniProt databases. Conclusion Our study suggests that the horizontal transfer of TMP/SMX resistance via class 1 integron is most frequently occurred within Enterobacteriaceae and has spread to a wide range of sources including soil, poultry, and marine water.

Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.

Certain commonly used compounds that interfere with the functions of the endocrine system are classified as endocrine-disrupting chemicals (EDCs). Bisphenol A (BPA) is an EDC that is widely used in food containers. BPA levels in human sera are commonly observed to be approximately 1-100 nM. Compared with the effects of BPA on the gonads, its effects on the adrenal gland are poorly understood. To investigate the influence of BPA on steroidogenesis, we examined the activity of the steroidogenic gene Cyp11a1 and its regulatory pathways in mouse Y1 adrenal cortex cells. Treatment with BPA at < 100 µM did not cause cell death. However, increased promoter activity and protein expression of Cyp11a1 were induced by low doses of BPA (10-1000 nM). Moreover, BPA induced c-Jun phosphorylation, and a specific inhibitor of c-Jun N-terminal kinase (JNK) significantly suppressed BPA-induced steroidogenesis. Thus, treatment of adrenal cells with low doses of BPA activated Cyp11a1 and increased corticosterone production through the JNK/c-Jun signaling pathway. Identical results were observed in rats after BPA injection. The abnormal induction of hormone synthesis by BPA in the adrenal gland might be linked to human metabolic defects and neuropsychiatric disorders.

This paper presents the Enhanced Bluetree, a mesh topology scheme for Bluetooth scatternet formation. The scatternet formation algorithm includes two phases. In the first phase, a designated node called the root starts to create a tree-shaped topology and in the second phase the tree-shaped topology is converted into a mesh-shaped topology. In addition, a return connection mechanism is introduced in this phase to generate more connection paths among the nodes. The mechanism contains two scatternet topology models including the slave/slave mesh (SSM) model and the master/slave mesh (MSM) model. The SSM Model builds a mesh-shaped topology by interconnecting more leaf nodes. On the other hand, the MSM Model connects additional intermediate nodes to establish the backbone connection in a mesh-shaped topology. Simulation results show that both the SSM and the MSM of an Enhanced Bluetree more effectively improve the network performance than Bluetree by significantly reducing the average path length.

Both 2D electromagnetic and electrical semiconductor simulations are performed sequentially in this study in order to better understand the structural principles of thin-film crystalline solar cells with back surface field and blaze diffractive grating. In the absence of adequate approximations for blazed gratings, we simulate silicon solar cells electromagnetically and electrically in order to deal with the geometrical complexity produced by the blazed grating with a BSF on top of it. Thin-film crystalline silicon solar cells (TF-c-Si SCs) typically exhibit poor quantum efficiency both at shorter wavelengths and longer wavelengths with sharp drops in spectral response. Longer wavelength spectral response (from 0.6 μm to 1.2 μm) is addressed here first by considering the influence of blaze gratings on the enhancement of effective optical absorption in thin-film crystalline silicon (TF-c-Si) solar cells. The effect of the back surface field layer (BSF) in terms of improving minority carrier collection is also taken into account. In the 2D electromagnetic simulation, polarization dependent two-dimensional (2D) numerical simulations based on rigorous coupled wave analysis (RCWA) and finite element method (FEM) are implemented for the optimization of optical absorption of the solar cell structure. A rather large tolerance in design parameters of the optimized blaze grating structure was found. The optimized blaze grating structures help in improving the cell efficiency, especially for weak absorption thin cell structures. The enhancement of equivalent optical path length reveals the efficient light trapping effect caused by the diffractions of the blaze grating structures, especially in the longer wavelength range. In the electrical semiconductor simulation, the BSF, which arises from the heavy acceptor doping that creates the concentration gradient, is set atop the blaze grating in order to provide an extra small drift field for the collection of minority electrons. Incorporating the optimized antireflection coating along with a BSF layer and a blaze-grating in the 2 μm cell doubles cell efficiency. The use of blazed gratings in thin-film solar cells, which can be performed upon silicon by means of lithography and ion-beam etching, is promising for low cost and high-efficient solar cell applications.

Substrate coupling in 3-D-ICs using Cu through silicon vias (TSVs) is a predicament widely documented in recent literature. Yet, discussions remain limited to the electromagnetic framework, such that a complete understanding of noise propagation and absorption is hampered. This letter thoroughly examines these phenomena in the TSVs from the integrated perspectives of semiconductor physics and electromagnetic theory and investigates the noise reduction method using the combination of p \(+\) guard-ring and grounded TSV via 3-D device simulation.

Post-traumatic stress disorder (PTSD) is a complex syndrome that is defined by individual exposed to intense, life-threatening trauma thereby leading to physical and psychological abnormalities. They further develop additional symptoms including persistent anxiety, exaggerated startle, cognitive impairments, and diminished extinction of fear. Most of the previous studies focused on brain and neurophysiology, but PTSD affects the whole body. Therefore, we wanted to concentrate more on the effects on sex hormones using rats. Testosterone and estradiol are major sex hormones in male and female which are well known to participate in not only reproduction but also brain function and behaviors. Two behavioral tests, open field test and tail suspension test, were used to determine whether animals have PTSD-like symptoms. At the same time, serum samples were collected for sex hormone analysis. We investigated the influences of traumatic stress and then tried to find out the correlations of behaviors and hormones. In results, 22% of rats were affected by stress based on the behavioral tests and grouped as PTSD-like. These rats showed enhanced anxiety and depression behaviors. In serum samples from the PTSD-like group, only estradiol levels in male after stress are significant higher than the control or stressed but no symptom groups. Testosterone level showed no difference after stress both in male and female. We also observed that only estradiol level in male correlates with PTSD-like behaviors. It indicates that estradiol levels in male just after traumatic stress might be an indicator for PTSD-like symptoms.

This paper presents simulation results of substrate noise coupling between through silicon via (TSV) and MOSFET. Electrical noise coupling through coexistence of junction capacitances and threshold modulation in substrate is studied and discussed through 2D and 3D transient analyses in this paper. Furthermore, noise isolation methods including guard rings and grounded shield TSV are incorporated to improve the noise decoupling and are examined to verify their effectiveness.

A novel equivalent circuit model of through-silicon via (TSV) considering the time-dependent capacitance due to metal-oxide-semiconductor (MOS) effect has been proposed. This model can characterize the variance of capacitance between metal and silicon substrate caused by the differential change of depletion region width as the voltage applied on the TSV changes with time. Compared to conventional TSV models, the capacitance has a 70% difference when the TSV's applied voltage transits from low state to high state. Besides, 3% difference of eye height and 100% difference of eye jitter can be observed in eye diagram by SPICE simulation.

This paper discusses the V-grooved surface texturing in terms of geometrical optics and uses Fresnel's formula to calculate the reflectivity. We count all possible reflections of light paths for different angles of incidence as well as structure's various tilt angles before summing them up together in order to obtain the total reflectivity. We discuss two different light path conditions as follows: 1) the path of light incidence falls perpendicularly onto the edges of the V grooves; 2) the path of light incidence in terms of its horizontal component when it approaches parallel with the edges of V grooves. We use TracePro simulation software in order to verify our analysis. The results from both methods are compatible, enabling us to conclude that light path's geometrical behavior correspond with our analysis of the V-grooved surface. For oblique incident light, V-grooved surface is proved to be effective in reducing the reflectivity for large angles of incidences.

This paper proposes a new method based on fuzzy logic theory to adjust the pulse width of PWM (Pulse Width Modulation) control in digital redesign and to implement it by FPGA (Field Programmable Gate Array) chip. The GA (Genetic Algorithm) is utilized to adjust the parameters of fuzzy logical system such that output response of controlled hybrid system closely matches with that of analog system.

This paper proposes a new method based on gradient operator together with interval arithmetic operations to converter a continuous-time chaotic nonlinear system to an equivalent discrete-time uncertain model. The bounds of interval system matrices via the proposed method are able to tightly enclose the exact nonlinear system. Finally we take a nonlinear chaotic circuit to illustrative our method's effectiveness.

Optical design in enhancing optical absorption of group-III-nitride- and multiple quantum well-based GaN/InxGa1-xN/cSi dual-junction tandem solar cells with triangular diffraction grating is simulated and optimized by using combined two-dimensional rigorous coupled wave analysis and transfer matrix methods. This paper thoroughly examines these phenomena of optical absorption affected by antireflection coatings, multiple thin-film layers and diffraction gratings with the integrated perspectives of semiconductor physics and electromagnetic theory for the first time. An improvement of 58% in absorption compared to the prototype SC is obtained which means more than 80% of incoming light (hυ > EgSi) can be harvested in this thin-film (< 4 μm in total) design.