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Long-read sequencing, exemplified by PacBio, revolutionizes genomics, overcoming challenges like repetitive sequences. However, the high DNA requirement (> 1 µg) is prohibitive for small organisms. We develop a low-input (100 ng), low-cost, and amplification-free library-generation method for PacBio sequencing (LILAP) using Tn5-based tagmentation and DNA circularization within one tube. We test LILAP with two Drosophila melanogaster individuals, and generate near-complete genomes, surpassing preexisting single-fly genomes. By analyzing variations in these two genomes, we characterize mutational processes: complex transpositions (transposon insertions together with extra duplications and/or deletions) prefer regions characterized by non-B DNA structures, and gene conversion of transposons occurs on both DNA and RNA levels. Concurrently, we generate two complete assemblies for the endosymbiotic bacterium Wolbachia in these flies and similarly detect transposon conversion. Thus, LILAP promises a broad PacBio sequencing adoption for not only mutational studies of flies and their symbionts but also explorations of other small organisms or precious samples. Pacific Biosciences (PacBio) High Fidelity (HiFi) long-read sequencing usually requires a relatively high amount of DNA input (> 1 µg). Here the authors develop LILAP, a Low-Input (100 ng), Low-cost, and Amplification-free library-generation method for PacBio sequencing, enabling the generation of two high-quality individual fly genomes. [ABSTRACT FROM AUTHOR]

Understanding how to increase soybean yield is crucial for global food security. The genetic and epigenetic factors influencing seed size, a major crop yield determinant, are not fully understood. We explore the role of DNA demethylase GmDMEa in soybean seed size. Our research indicates that GmDMEa negatively correlates with soybean seed size. Using CRISPR-Cas9, we edited GmDMEa in the Dongnong soybean cultivar, known for small seeds. Modified plants had larger seeds and greater yields without altering plant architecture or seed nutrition. GmDMEa preferentially demethylates AT-rich transposable elements, thus activating genes and transcription factors associated with the abscisic acid pathway, which typically decreases seed size. Chromosomal substitution lines confirm that these modifications are inheritable, suggesting a stable epigenetic method to boost seed size in future breeding. Our findings provide insights into epigenetic seed size control and suggest a strategy for improving crop yields through the epigenetic regulation of crucial genes. This work implies that targeted epigenetic modification has practical agricultural applications, potentially enhancing food production without compromising crop quality. A study on a soybean DNA demethylase reveals that seed size is negatively regulated by GmDMEa, which is closely linked to methylation on transposon elements. [ABSTRACT FROM AUTHOR]

This study aims to promote the protection and inheritance of cultural heritage in private gardens in the Jiangnan area of China. By establishing a precise visual labeling system and accelerating the construction of a database for private garden features, we deepen the understanding of garden design philosophy. To this end, we propose an improved Jiangnan private garden recognition model based on You Only Look Once (YOLO) v8. This model is particularly suitable for processing garden environments with characteristics such as single or complex structures, rich depth of field, and cluttered targets, effectively enhancing the accuracy and efficiency of object recognition. This design integrates the Diverse Branch Block (DBB), Bidirectional Feature Pyramid Network (BiFPN), and Dynamic Head modules (DyHead) to optimize model accuracy, feature fusion, and object detection representational capability, respectively. The enhancements elevated the model's accuracy by 8.7%, achieving a mean average precision (mAP@0.5) value of 57.1%. A specialized dataset, comprising 4890 images and encapsulating various angles and lighting conditions of Jiangnan private gardens, was constructed to realize this. Following manual annotation and the application of diverse data augmentation strategies, the dataset bolsters the generalization and robustness of the model. Experimental outcomes reveal that, compared to its predecessor, the improved model has witnessed increments of 15.16%, 3.25%, and 11.88% in precision, mAP0.5, and mAP0.5:0.95 metrics, respectively, demonstrating exemplary performance in the accuracy and real-time recognition of garden target elements. This research not only furnishes robust technical support for the digitization and intelligent research of Jiangnan private gardens but also provides a potent methodological reference for object detection and classification research in analogous domains. [ABSTRACT FROM AUTHOR]

Hafnium oxide-based ferroelectric field-effect-transistors (FeFET), which combine super-steep logical switching and low power non-volatile memory functions, have significant potential for post-Moore integrated circuit innovations with higher energy efficiency and larger integration scale. In this review, recent research into hafnium oxide-based ferroelectric (FE) films and different functional devices is presented, from fundamentals to applications. Different technological challenges and state-of-the-art research and development efforts related to the physical understanding and performance optimization of FE films, advanced hafnium oxide-based device integration, and device applications in logic-in-memory and artificial synapses and neurons for neuromorphic computing are addressed. [ABSTRACT FROM AUTHOR]

Benzotriazoles (BTs) are highly produced chemicals that are commonly used in the manufacture of aircraft de-icing/antifreeze fluids (ADAFs), coolants, etc. BTs have been detected in a variety of water environments, causing health hazards to aquatic species and humans. In this study, 1H-benzotriazole (BTri) and 4-methyl-1H-benzotriazole (4-TTri) were selected to investigate their degradation mechanisms in the aqueous phase initiated by ·OH using a theoretical calculation method. Addition reactions are the main type of reactions of ·OH with BTri and 4-TTri. The total rate constants for the reactions of BTri and 4-TTri with ·OH at 298 K are 8.26 × 109 M−1 s−1 and 1.81 × 1010 M−1 s−1, respectively. The reaction rate constants increase as the temperature rises, indicating that rising temperatures promote the degradation of BTri and 4-TTri. 7-hydroxy-1H-benzotriazole (1-P1) and 4-hydroxy-benzotriazoles (1-P2) produced via multiple reaction pathways are important transformation products of BTri. After successive reactions with ·OH, 1-P1 and 1-P2 can be successively converted to 4,7-dihydroxy-1H-benzotriazole (1-P7), 4,7-dione-1H-benzotriazole (1-P8), and 1,2,3-triazole-4,5-dicarboxylic acid (1-P9), which is consistent with the product compositions detected in the experiments. The toxicity assessment indicated that the acute toxicity and chronic toxicity of the resulting transformation products are significantly reduced compared to BTri as the degradation process progressed, and ultimately showed no harm to all three aquatic organisms (fish, daphnia, and green algae). Hence, advanced oxidation processes (AOPs) can not only effectively remove BTs from water, but also reduce their toxic effects on aquatic organisms. [ABSTRACT FROM AUTHOR]

The Betula genus contains pentacyclic triterpenoid betulin known for its environmental adaptation and medicinal properties. However, the mechanisms underlying betulin biosynthesis responding to climate change remain unclear. In this study, the role of epigenetic modification (DNA methylation) in betulin biosynthesis was examined and how climatic factors influence it. Whole-genome bisulfite sequencing was performed for greenhouse-grown Chinese white birch (Betula platyphylla Sukaczev) treated with DNA methylation inhibitor zebularine (ZEB) and a natural birch population in Northeast China. ZEB treatment significantly affected the CHH methylation level of transposable elements and betulin content in a hormesis dose-dependent manner. The methylation and expression of bHLH9, a key transcriptional factor controlling betulin biosynthesis, were also consistently affected by ZEB treatment as a hormetic dose–response. In the natural population, there was a positive correlation between promoter methylation of bHLH9 and summer precipitation, while winter temperature was negatively correlated. Thus climate-dependent methylation of bHLH9 regulates the expression of downstream genes involved in betulin biosynthesis. This study highlights the role of environmental signals to induce epigenetic changes that result in betulin production, possibly helping to develop resilient plants to combat ongoing climate change and enhance secondary metabolite production. [ABSTRACT FROM AUTHOR]

In this work, extremely thin silicon-on-insulator field effective transistors (ETSOI FETs) are fabricated with an ultra-thin 3 nm ferroelectric (FE) hafnium zirconium oxides (Hf0.5Zr0.5O2) layer. Furthermore, the subthreshold characteristics of the devices with double gate modulation are investigated extensively. Contributing to the advantages of the back-gate voltage coupling effects, the minimum subthreshold swing (SS) value of a 40 nm ETSOI device could be adjusted from the initial 80.8–50 mV/dec, which shows ultra-steep SS characteristics. To illustrate this electrical character, a simple analytical model based on the transient Miller model is demonstrated. This work shows the feasibility of FE ETSOI FET for ultra-low-power applications with dynamic threshold adjustment. [ABSTRACT FROM AUTHOR]

Exosomes are highly important in clinical diagnosis due to their high homology with their parental cells. However, conventional exosome detection methods still face the challenges of expensive equipment, low sensitivity, and complex procedures. Field effect transistors (FETs) are not only the most essential electronic component in the modern microelectronics industry but also show great potential for biomolecule detection owing to the advantages of rapid response, high sensitivity, and label-free detection. In this study, we proposed a Si nanowire field-effect transistor (Si-NW Bio-FET) device chemically modified with specific antibodies for the electrical and label-free detection of exosomes. The Si-NW FETs were fabricated by standard microelectronic processes with 45 nm width nanowires and packaged in a polydimethylsiloxane (PDMS) microfluidic channel. The nanowires were further modified with the specific CD63 antibody to form a Si-NW Bio-FET. The use of the developed Si-NW Bio-FET for the electrical and label-free detection of exosomes was successfully demonstrated with a limit of detection (LOD) of 2159 particles/mL. In contrast to other technologies, in this study, Si-NW Bio-FET provides a unique strategy for directly quantifying and real-time detecting exosomes without labeling, indicating its potential as a tool for the early diagnosis of cancer. [ABSTRACT FROM AUTHOR]

WSe2 is thought to be one of the best emerging p-type transition metal dichalcogenide (TMD) materials for potential low-power complementary metal oxide semiconductor (CMOS) circuit applications. However, the contact barrier and the interface quality hinder the performance of p-type field effect transistors (FETs) with WSe2 films. In this work, metals with different work functions—Pd, Pt, and Ag—were systematically investigated as contacts for WSe2 to decrease the contact resistances at source/drain electrodes and potentially improve transistor performance. Optimized p-type multilayer WSe2 FETs with Pd contacts were successfully fabricated, and excellent electrical characteristics were obtained: a hole mobility of 36 cm2V−1 s−1; a high on/off ratio, over 106; and a record low sub-threshold swing, SS = 95 mV/dec, which may be attributed to the small Schottky barrier height of 295 meV between Pd and WSe2, and strong Fermi-level pinning near the top of the valence band at the interface. Finally, a full-functional CMOS inverter was also demonstrated, consisting of a p-type WSe2 FET together with a normal n-type MoS2 FET. This confirmed the potential of TMD FETs in future low-power CMOS digital circuit applications. [ABSTRACT FROM AUTHOR]

In this work, a selective wet etching process of Si to Si0.7Ge0.3 with TMAH solution to fabricate SiGe nanowires is systematically investigated. Initially, the 2.3% TMAH solution at 20 °C is applied for the as grown Si0.7Ge0.3/Si multilayers stack and a "rectangular" profile is achieved at the Si0.7Ge0.3 extremity due to its high selectivity. However, the reduction of Ge concentration due to the Ge interdiffusion caused by the high temperature anneal treatment will attain a reduced selectivity of Si to Si0.7Ge0.3 and a "rounding" Si0.7Ge0.3 extremity profile. Moreover, the profile of the upper Si0.7Ge0.3 extremity is clearly worse than the bottom one. This is because the Ge concentration of upper Si0.7Ge0.3 is 1.5% lower and the Ge interdiffusion of the upper Si0.7Ge0.3 is slightly worse. After increasing the TMAH concentration to 25%, both the upper and bottom Si0.7Ge0.3 extremity can achieve a "rectangular" extremity profile with an almost the same Si0.7Ge0.3 loss ~ 1.5 nm per side. Compared with 2.3% TMAH concentration, the Ge concentration of the etching off SiGe film can be reduced from lower than 29% to lower than 24% using the 25% TMAH solution at 20 °C. Therefore, the 25% TMAH solution at 20 °C is chosen as the optimal selective etching condition for the thermal treated Si0.7Ge0.3/Si multilayers stack samples. Finally, a vertical stacked double SiGe nanowire structure is successfully prepared by utilizing this optimal process condition. This indicates that it is a practicable technique for the selective wet etching of Si in fabricating SiGe nanowires. [ABSTRACT FROM AUTHOR]

In this work, SiGe Fin formation technique using shallow trench isolation (STI) first or STI last strategy for the high mobility channel FinFET device is systematically investigated. A 20 nm width and 35 nm height high crystalline quality of the Si0.7Ge0.3 Fin formation for STI first scheme is demonstrated by utilizing a new developed Si Fin etching, Si Fin recess and SiGe selective epitaxial growth process. For the STI last strategy, a novel chemical mechanical planarization (CMP) treated three-layer SiGe strain relaxed buffer (SRB) is successfully fabricated and a 50 nm high crystal quality and atomically smooth surface Si0.5Ge0.5 layer on this SRB is attained. Moreover, a spike annealing is employed to avoid the Si0.5Ge0.5 Fin oxidation during STI densification with an acceptable STI etching rate. However, both a spike annealing and a lower temperature of traditional furnace at 850 °C or 750 °C suffer micro-trench issue during the Fin reveal process. Therefore, a new developed process, named as STI recess first, is developed to resolve both thermal instability and micro-trench issue at the same time. A minor Si0.5Ge0.5 Fin loss with a sharp Si0.7Ge0.3 SRB/Si0.5Ge0.5 interfaces for STI last scheme is realized by utilizing this new developed STI recess first process. [ABSTRACT FROM AUTHOR]

In this work, a novel three-layer SiGe strain relaxed buffer/strained Si0.5Ge0.5 layer stacking structure is systematically investigated. The novel three-layer graded SiGe strain relaxed buffer, whose Ge concentration increased from bottom to top by roughly 10% with an in situ annealing after each layer grown, can effectively constrain the threading dislocation in the strain relaxed buffer layer. Moreover, a chemical mechanical planarization process can be applied to the strain relaxed buffer to further improve its surface roughness. A high crystal quality and atomically smooth surface Si0.5Ge0.5 layer can be successfully realized on the novel chemical mechanical planarization-treated three-layer SiGe strain relaxed buffer. This strategy can attain at least 50 nm and 0.6% compressive strained Si0.5Ge0.5 layer and its quantification of the strain level is confirmed by utilizing the scanning moiré fringe imaging technique. It can be seen that this novel structure can provide a better mobility and larger width for the FinFET or nanowire SiGe channel device. [ABSTRACT FROM AUTHOR]

Halogenated biphenyls are worldwide persistent pollutants of great environmental concern. In particular, polychlorinated biphenyls and polybrominated biphenyls have been globally used for industrial purposes until they were found highly toxic, mutagenic and carcinogenic to humans. Therefore, ecological strategies to remove halogenated biphenyls, such as enzyme-catalyzed degradation, are needed. Here, we studied the effect of substitution of F, Cl, Br or I at the 4,4′-positions of 2,3-dihydro-2,3-dihydroxybiphenyl-2,3-dehydrogenase (BphB) on the degradation of halogenated biphenyls by quantum and molecular mechanics. Results show that Boltzmann-weighted average degradation barriers of substituted BphB are all lower than the unsubstituted biphenyl, except for chlorinated biphenyl. The roles of residues nearby the active site, e.g., isoleucine89, asparagine115, serine142, asparagine143, proline184, methionine187 and threonine189, were also investigated. [ABSTRACT FROM AUTHOR]

Phorate, an extremely hazardous organophosphorus insecticide, is still widely used in many countries and territories currently. It may be released in the atmosphere where it can undergo transport and chemical transformations. In this study, the reaction mechanism for the OH-initiated atmospheric oxidation of phorate was investigated. The geometrical parameters and vibrational frequencies of all the stationary points were calculated at the MPWB1K level with the 6-31G(d,p) basis set. Single-point energy calculations were carried out at the MPWB1K/6-311+G(3df,2p) level. Canonical variational transition-state theory with small curvature tunneling contribution was used to calculate the rate constants over the temperature range of 200-370 K. The Arrhenius formulas were fitted. The results indicate that the channel of the formation of phorate oxon resulting from OH addition to phorate, and H abstractions from the -CH- portion of the -CHCH group in phorate are energetically favorable. The main degradation products include phorate oxon, SO. [ABSTRACT FROM AUTHOR]

To understand the size-resolved aerosol ionic composition and the factors influencing secondary aerosol formation in the upper boundary layer in South Central China, size-segregated aerosol samples were collected using a micro-orifice uniform deposit impactor (MOUDI) in spring 2009 at the summit of Mount Heng (1269 m asl), followed by subsequent laboratory analyses of 13 inorganic and organic water-soluble ions. During non-dust-storm periods, the average PM 1.8 concentration was 41.8 μg·m -3, contributing to 55% of the PM 10. Sulfates, nitrates, and ammonium, the dominant ions in the fine particles, amounted to 46.8% of the PM 1.8. Compared with Mount Tai in the North China Plain, the concentrations of both fine and coarse particles and the ions contained therein were substantially lower. When the air masses from Southeast Asia prevailed, intensive biomass burning there led to elevated concentrations of sulfates, nitrates, ammonium, potassium, and chloride in the fine particles at Mount Heng. The air masses originating from the north Gobi brought heavy dust storms that resulted in the remarkable production of sulfates, ammonium, methane sulfonic acid, and oxalates in the coarse particles. Generally, the sulfates were primarily produced in the form of (NH 4) 2SO 4 in the droplet mode via heterogeneous aqueous reactions. Only approximately one-third of the nitrates were distributed in the fine mode, and high humidity facilitated the secondary formation of fine nitrates. The heterogeneous formation of coarse nitrates and ammonium on dry alkaline dust surfaces was found to be less efficient than that on the coarse particles during non-dust-storm periods. [ABSTRACT FROM AUTHOR]

For the 2008 Olympic Games, drastic control measures were implemented on industrial and urban emissions of sulfur dioxide (SO), nitrogen oxides (NO) and other pollutants to address the issues of poor air quality in Beijing. To investigate the effects of SO and NO reductions on the particulate sulfate and nitrate concentrations as well as their size distributions, size-segregated aerosol samples were collected using micro-orifice uniform deposit impactors (MOUDIs) at urban and downwind rural sites in Beijing before and after full-scale controls. During the sampling period, the mass concentrations of fine particles (PM) at the urban and rural sites were 94.0 and 85.9 μg m, respectively. More than 90% of the sulfates and ∼60% of nitrates formed as fine particles. Benefiting from the advantageous meteorological conditions and the source controls, sulfates were observed in rather low concentrations and primarily in condensation mode during the Olympics. The effects of the control measures were separately analyzed for the northerly and the southerly air-mass-dominated days to account for any bias. After the control measures were implemented, PM, sulfates, and nitrates were significantly reduced when the northerly air masses prevailed, with a higher percentage of reduction in larger particles. The droplet mode particles, which dominated the sulfates and nitrates before the controls were implemented, were remarkably reduced in mass concentration after the control measures were implemented. Nevertheless, when the polluted southerly air masses prevailed, the local source control measures in Beijing did not effectively reduce the ambient sulfate concentration due to the enormous regional contribution from the North China Plain. [ABSTRACT FROM AUTHOR]

Near real-time measurements of PM ionic compositions were performed at the summit of the highest mountain in the central-eastern plains in the spring and summer of 2007 in order to characterize aerosol composition and its interaction with clouds. The average concentrations of total water soluble ions were 27.5 and 36.7 μg m, accounting for 44% and 62% of the PM mass concentration in the spring and summer, respectively. A diurnal pattern of SO, NH and NO was observed in both campaigns and attributed to the upslope/downslope transport of air mass and the development of the planetary boundary layer (PBL). The average SO oxidation ratio (SOR) in summer was 57% (±27%), more than twice that in spring 24% (±16%); the fine nitrate oxidation ratio (NOR) was comparable in the two seasons (9 ± 6% and 11 ± 10% in summer and spring, respectively). This result indicates strong summertime production of sulfate aerosol. A principal component analysis shows that short-range and long-range transport of pollution, cloud processing, and crustal source were the main factors affecting the variability of the measured ions (and other trace gases and aerosols) at Mt. Tai. Strong indications of biomass burning were observed in summer. Cloud scavenging rates showed larger variations for different ions and in different cloud events. The elevated concentrations of the water soluble ions at Mt. Tai indicate serious aerosol pollution over the North China plain of eastern China. [ABSTRACT FROM AUTHOR]

The reaction of disilane with atomic hydrogen has been studied. This reaction involves both substitution and abstraction. Calculations show that the hydrogen abstraction is the strongest competing channel. The canonical variational transition state theory with a small curvature tunneling correction (SCT) has been used for the kinetic calculation. The theoretical results are in good agreement with the available experimental data. Comparing the reactions of atomic hydrogen with disilane and silane, it can be seen that the reactivity of the Si-H bond is higher in Si2H6 than that in SiH4. [ABSTRACT FROM AUTHOR]

Main conclusion: In ddm1 mutants, the DNA methylation is primarily affected in the heterochromatic region of the chromosomes, which is associated with the segregation distortion of SNPs in the F2 progenies. Segregation distortion (SD) is common in most genetic mapping experiments and a valuable resource to determine how gene loci induce deviation. Meiotic DNA crossing over and SD are under the control of several types of epigenetic modifications. DNA methylation is an important regulatory epigenetic modification that is inherited across generations. In the present study, we investigated the relationship between SD and DNA methylation. The ecotypes Col-0/C24 and chromatin remodeler mutants ddm1-10/Col and ddm1-15/C24 were reciprocally crossed to obtain F2 generations. A total of 300 plants for each reciprocally crossed plant in the F2 generations were subjected to next-generation sequencing to detect the single-nucleotide polymorphisms (SNPs) as DNA markers. All SNPs were analyzed using the Chi-square test method to determine their segregation ratio in F2 generations. Through the segregation ratio, whole-genome SNPs were classified into 16 classes. In class 10, the SNPs in the reciprocal crosses of wild type showed the expected Mendelian ratio of 1:2:1, while those in the reciprocal crosses of ddm1 mutants showed distortion. In contrast, all SNPs in class 16 displayed a normal 1:2:1 ratio, and class 1 showed SD, regardless of wild type or mutants, as assessed using CAPS (cleaved amplified polymorphic sequences) marker analysis to confirm the next-generation sequencing. In ddm1 mutants, the DNA methylation is highly reduced throughout the whole genome and more significantly in the heterochromatic regions of chromosomes. Our results showed that the ddm1 mutants exhibit low levels of DNA methylation, which facilitates the SD of SNPs primarily located in the heterochromatic region of chromosomes by reducing the heterozygous ratio. The present study will provide a strong base for future research focusing on the impact of DNA methylation on trait segregation and plant evolution. [ABSTRACT FROM AUTHOR]

The original version of this article unfortunately contained a mistake. The sequence of the author affiliations was incorrect. The correct information is given below. [ABSTRACT FROM AUTHOR]

Polycyclic aromatic hydrocarbons (PAHs) have induced large-scale and long-term environmental contamination due to heavy emissions, toxicity, and persistence. The investigation of the ultimate sink of PAHs in the atmosphere is very important. In this work, using quantum chemistry methods, the reaction mechanism of hydroxyl radical-initiated oxidation of benzo[a]anthracene (BaA) in the atmosphere was studied. The products resulted from the gas-phase reaction of BaA with hydroxyl radical include benzo[a]anthracenols, dialdehydes, ketones, epoxides, etc. Applying Rice-Ramsperger-Kassel-Marcus (RRKM) theory, the overall rate constant for reactions of •OH addition to BaA was estimated to be 4.82 × 10−11 cm3 molecule−1 s−1 at 298 K and 1 atm. The lifetime of BaA in the atmosphere with respect to hydroxyl radical was calculated to be 5.92 h. [ABSTRACT FROM AUTHOR]

A correction is presented to the article "Polluted dust promotes new particle formation and growth."