Transformer with difference convolutional network for lightweight universal boundary detection.

Although deep-learning methods can achieve human-level performance in boundary detection, their improvements mostly rely on larger models and specific datasets, leading to significant computational power consumption. As a fundamental low-level vision task, a single model with fewer parameters to achieve cross-dataset boundary detection merits further investigation. In this study, a lightweight universal boundary detection method was developed based on convolution and a transformer. The network is called a "transformer with difference convolutional network" (TDCN), which implies the introduction of a difference convolutional network rather than a pure transformer. The TDCN structure consists of three parts: convolution, transformer, and head function. First, a convolution network fused with edge operators is used to extract multiscale difference features. These pixel difference features are then fed to the hierarchical transformer as tokens. Considering the intrinsic characteristics of the boundary detection task, a new boundary-aware self-attention structure was designed in the transformer to provide inductive bias. By incorporating the proposed attention loss function, it introduces the direction of the boundary as strongly supervised information to improve the detection ability of the model. Finally, several head functions with multiscale feature inputs were trained using a bidirectional additive strategy. In the experiments, the proposed method achieved competitive performance on multiple public datasets with fewer model parameters. A single model was obtained to realize universal prediction even for different datasets without retraining, demonstrating the effectiveness of the method. The code is available at https://github.com/neulmc/TDCN.

Knot Architecture for Biocompatible and Semiconducting 2D Electronic Fiber Transistors.

Wearable devices have generally been rigid due to their reliance on silicon-based technologies, while future wearables will utilize flexible components for example transistors within microprocessors to manage data. Two-dimensional (2D) semiconducting flakes have yet to be investigated in fiber transistors but can offer a route toward high-mobility, biocompatible, and flexible fiber-based devices. Here, the electrochemical exfoliation of semiconducting 2D flakes of tungsten diselenide (WSe2) and molybdenum disulfide (MoS2) is shown to achieve homogeneous coatings onto the surface of polyester fibers. The high aspect ratio (>100) of the flake yields aligned and conformal flake-to-flake junctions on polyester fibers enabling transistors with mobilities µ ≈1 cm2 V-1 s-1 and a current on/off ratio, Ion/Ioff ≈102-104. Furthermore, the cytotoxic effects of the MoS2 and WSe2 flakes with human keratinocyte cells are investigated and found to be biocompatible. As an additional step, a unique transistor 'knot' architecture is created by leveraging the fiber diameter to establish the length of the transistor channel, facilitating a route to scale down transistor channel dimensions (≈100 µm) and utilize it to make a MoS2 fiber transistor with a human hair that achieves mobilities as high as µ ≈15 cm2 V-1 s-1.

All-fiber hectowatt radially polarized laser system.

A high-power all-fiber radially polarized laser system is demonstrated, in which an integrated nanograting mode convertor (S-wave plate) is used for the generation of radially polarized beam. Experimentally, a 1-W radially polarized beam was used as the seed laser, whose mode purity and mode extinction ratio (MER) were 96.5% and 98.3%, respectively. A single-stage few-mode fiber amplifier was employed to boost the 1-W seed laser to an average power of 113.2 W, when the pump power was 160 W. The corresponding slope efficiency and beam quality factor (M2) were approximately 72% and 2.3%, respectively. Moreover, the mode purity and MER of the amplified radially polarized laser were measured to be 95.7% and 97%, respectively. To the best of our knowledge, this is the highest output power from an all-fiber radially polarized laser system without obvious degradations of the mode purity and MER.

Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome.

Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that is responsible for major health and economic costs worldwide1. Mtb encounters diverse environments during its life cycle and responds to these changes largely by reprogramming its transcriptional output2. However, the mechanisms of Mtb transcription and how they are regulated remain poorly understood. Here we use a sequencing method that simultaneously determines both termini of individual RNA molecules in bacterial cells3 to profile the Mtb transcriptome at high resolution. Unexpectedly, we find that most Mtb transcripts are incomplete, with their 5' ends aligned at transcription start sites and 3' ends located 200-500 nucleotides downstream. We show that these short RNAs are mainly associated with paused RNA polymerases (RNAPs) rather than being products of premature termination. We further show that the high propensity of Mtb RNAP to pause early in transcription relies on the binding of the σ-factor. Finally, we show that a translating ribosome promotes transcription elongation, revealing a potential role for transcription-translation coupling in controlling Mtb gene expression. In sum, our findings depict a mycobacterial transcriptome that prominently features incomplete transcripts resulting from RNAP pausing. We propose that the pausing phase constitutes an important transcriptional checkpoint in Mtb that allows the bacterium to adapt to environmental changes and could be exploited for TB therapeutics.

Quantitative analysis of printed nanostructured networks using high-resolution 3D FIB-SEM nanotomography.

Networks of solution-processed nanomaterials are becoming increasingly important across applications in electronics, sensing and energy storage/generation. Although the physical properties of these devices are often completely dominated by network morphology, the network structure itself remains difficult to interrogate. Here, we utilise focused ion beam - scanning electron microscopy nanotomography (FIB-SEM-NT) to quantitatively characterise the morphology of printed nanostructured networks and their devices using nanometre-resolution 3D images. The influence of nanosheet/nanowire size on network structure in printed films of graphene, WS2 and silver nanosheets (AgNSs), as well as networks of silver nanowires (AgNWs), is investigated. We present a comprehensive toolkit to extract morphological characteristics including network porosity, tortuosity, specific surface area, pore dimensions and nanosheet orientation, which we link to network resistivity. By extending this technique to interrogate the structure and interfaces within printed vertical heterostacks, we demonstrate the potential of this technique for device characterisation and optimisation.

When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions.

Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field. Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Targeting PAK4 reverses cisplatin resistance in NSCLC by modulating ER stress.

Chemoresistance poses a significant impediment to effective treatments for non-small-cell lung cancer (NSCLC). P21-activated kinase 4 (PAK4) has been implicated in NSCLC progression by invasion and migration. However, the involvement of PAK4 in cisplatin resistance is not clear. Here, we presented a comprehensive investigation into the involvement of PAK4 in cisplatin resistance within NSCLC. Our study revealed enhanced PAK4 expression in both cisplatin-resistant NSCLC tumors and cell lines. Notably, PAK4 silencing led to a remarkable enhancement in the chemosensitivity of cisplatin-resistant NSCLC cells. Cisplatin evoked endoplasmic reticulum stress in NSCLC. Furthermore, inhibition of PAK4 demonstrated the potential to sensitize resistant tumor cells through modulating endoplasmic reticulum stress. Mechanistically, we unveiled that the suppression of the MEK1-GRP78 signaling pathway results in the sensitization of NSCLC cells to cisplatin after PAK4 knockdown. Our findings establish PAK4 as a promising therapeutic target for addressing chemoresistance in NSCLC, potentially opening new avenues for enhancing treatment efficacy and patient outcomes.

Establishment of Coloproctitis Cancer Model in Mice and Evaluation of Therapeutic Effect of Chinese Medicine.

Colorectal cancer (CRC) is a common malignancy of the digestive system and has become the third most common malignancy worldwide and the second leading cause of malignancy-related death. Ulcerative coloproctitis (UC) is a precancerous lesion, and UC-associated CRC (UC-CRC) is the most common subtype of CRC. Therefore, a reasonable UC-CRC model is the cornerstone and guarantee of new drug development. Traditional Chinese medicine (TCM) has been widely used in the treatment of UC-CRC due to its good efficacy. As a classic tonic prescription of TCM, Liujunzi decoction (LJZD) has been widely used in the treatment of UC-CRC. In this study, a UC-CRC model was established by combining azomethane and dextran sulfate sodium, and the LJZD was administered. The data confirmed that LJZD can effectively inhibit cancer transition in UC-CRC by using mouse body weight, colorectal length, pathological and inflammatory factors, colorectal barrier function, and cancer markers. This protocol provides a system for evaluating the efficacy of TCM in the prevention and treatment of UC-CRC.

Coherent beam combining of cylindrical vector beams for power scaling.

Coherent beam combining (CBC) of cylindrical vector beams (CVBs) based on an active phase controller is proposed and demonstrated. Experimentally, two pieces of spatially variant wave plates (S-wave plate) were employed as vector mode convertors for two individual 1064-nm fiber amplifier channels. When the system was in a closed loop, a combined output power of 10 W and a CBC efficiency of higher than 94% were achieved, for both TM01 (radially polarized) mode and TE01 (azimuthally polarized) mode cases. Moreover, the laser system showed a high vector mode purity, which was measured to be ∼97.4% (TM01) and ∼97.3% (TE01). To the best of knowledge, this could possibly be the first demonstration of CBC of CVBs, which paves the way for power scaling of CVBs.

Solution-Processed Heterojunction Photodiodes Based on WSe2 Nanosheet Networks.

Solution-processed photodetectors incorporating liquid-phase-exfoliated transition metal dichalcogenide nanosheets are widely reported. However, previous studies mainly focus on the fabrication of photoconductors, rather than photodiodes which tend to be based on heterojunctions and are harder to fabricate. Especially, there are rare reports on introducing commonly used transport layers into heterojunctions based on nanosheet networks. In this study, a reliable solution-processing method is reported to fabricate heterojunction diodes with tungsten selenide (WSe2 ) nanosheets as the optical absorbing material and PEDOT: PSS and ZnO as injection/transport-layer materials. By varying the transport layer combinations, the obtained heterojunctions show rectification ratios of up to ≈104 at ±1 V in the dark, without relying on heavily doped silicon substrates. Upon illumination, the heterojunction can be operated in both photoconductor and photodiode modes and displays self-powered behaviors at zero bias.

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.

SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/H4K20me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation. It is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes, suggesting that the enzyme likely has uncharacterized non-catalytic activities. Our cryoelectron microscopy (cryo-EM), biochemical, biophysical, and cellular analyses reveal how SUV420H1 recognizes its nucleosome substrates, and how histone variant H2A.Z stimulates its catalytic activity. SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from the histone octamer, which is a non-catalytic activity. We hypothesize that this regulates the accessibility of large macromolecular complexes to chromatin. We show that SUV420H1 can promote chromatin condensation, another non-catalytic activity that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.

Age-related decline in hippocampal tyrosine phosphatase PTPRO is a mechanistic factor in chemotherapy-related cognitive impairment.

Chemotherapy-related cognitive impairment (CRCI) or "chemo brain" is a devastating neurotoxic sequela of cancer-related treatments, especially for the elderly individuals. Here we show that PTPRO, a tyrosine phosphatase, is highly enriched in the hippocampus, and its level is tightly associated with neurocognitive function but declined significantly during aging. To understand the protective role of PTPRO in CRCI, a mouse model was generated by treating Ptpro-/- female mice with doxorubicin (DOX) because Ptpro-/- female mice are more vulnerable to DOX, showing cognitive impairments and neurodegeneration. By analyzing PTPRO substrates that are neurocognition-associated tyrosine kinases, we found that SRC and EPHA4 are highly phosphorylated/activated in the hippocampi of Ptpro-/- female mice, with increased sensitivity to DOX-induced CRCI. On the other hand, restoration of PTPRO in the hippocampal CA3 region significantly ameliorate CRCI in Ptpro-/- female mice. In addition, we found that the plant alkaloid berberine (BBR) is capable of ameliorating CRCI in aged female mice by upregulating hippocampal PTPRO. Mechanistically, BBR upregulates PTPRO by downregulating miR-25-3p, which directly targeted PTPRO. These findings collectively demonstrate the protective role of hippocampal PTPRO against CRCI.

Structure and DNA-bridging activity of the essential Rec114-Mei4 trimer interface.

The DNA double-strand breaks (DSBs) that initiate meiotic recombination are formed by an evolutionarily conserved suite of factors that includes Rec114 and Mei4 (RM), which regulate DSB formation both spatially and temporally. In vivo, these proteins form large immunostaining foci that are integrated with higher-order chromosome structures. In vitro, they form a 2:1 heterotrimeric complex that binds cooperatively to DNA to form large, dynamic condensates. However, understanding of the atomic structures and dynamic DNA binding properties of RM complexes is lacking. Here, we report a structural model of a heterotrimeric complex of the C terminus of Rec114 with the N terminus of Mei4, supported by nuclear magnetic resonance experiments. This minimal complex, which lacks the predicted intrinsically disordered region of Rec114, is sufficient to bind DNA and form condensates. Single-molecule experiments reveal that the minimal complex can bridge two or more DNA duplexes and can generate force to condense DNA through long-range interactions. AlphaFold2 predicts similar structural models for RM orthologs across diverse taxa despite their low degree of sequence similarity. These findings provide insight into the conserved networks of protein-protein and protein-DNA interactions that enable condensate formation and promote formation of meiotic DSBs.

Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes.

Methyl-CpG-binding protein 2 (MeCP2) is an essential chromatin-binding protein whose mutations cause Rett syndrome (RTT), a leading cause of monogenic intellectual disabilities in females. Despite its significant biomedical relevance, the mechanism by which MeCP2 navigates the chromatin epigenetic landscape to regulate chromatin structure and gene expression remains unclear. Here, we used correlative single-molecule fluorescence and force microscopy to directly visualize the distribution and dynamics of MeCP2 on a variety of DNA and chromatin substrates. We found that MeCP2 exhibits differential diffusion dynamics when bound to unmethylated and methylated bare DNA. Moreover, we discovered that MeCP2 preferentially binds nucleosomes within the context of chromatinized DNA and stabilizes them from mechanical perturbation. The distinct behaviors of MeCP2 at bare DNA and nucleosomes also specify its ability to recruit TBLR1, a core component of the NCoR1/2 co-repressor complex. We further examined several RTT mutations and found that they disrupt different aspects of the MeCP2-chromatin interaction, rationalizing the heterogeneous nature of the disease. Our work reveals the biophysical basis for MeCP2's methylation-dependent activities and suggests a nucleosome-centric model for its genomic distribution and gene repressive functions. These insights provide a framework for delineating the multifaceted functions of MeCP2 and aid in our understanding of the molecular mechanisms of RTT.

Thermal Conductivity of Polyvinylidene Fluoride Films with a Multi-Scale Framework.

The orientation of amorphous regions in pure polymers has been noted to be critical to the enhancement of thermal conductivity (TC), but the available reports are still rather few. Here, we propose to prepare a polyvinylidene fluoride (PVDF) film with a multi-scale framework by introducing anisotropic amorphous nanophases in the form of cross-planar alignments among the in-planar oriented extended-chain crystals (ECCs) lamellae, which show an enhanced TC of 1.99 Wm-1 K-1 in the through-plane direction (K⟂) and 4.35 Wm-1 K-1 in the in-plane direction (K∥). Structural characterization determination using scanning electron microscopy and high-resolution synchrotron X-ray scattering showed that shrinking the dimension of the amorphous nanophases can effectively reduce entanglement and lead to alignments formation. Moreover, the thermal anisotropy of the amorphous region is quantitatively discussed with the aid of the two-phase model. Superior thermal dissipation performances are intuitively displayed by means of finite element numerical analysis and heat exchanger applications. Moreover, such unique multi-scale architecture also results in significant benefit in the improvement of dimensional stability and thermal stability. This paper provides a reasonable solution for fabricating inexpensive thermal conducting polymer films from the perspective of practical applications.

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.

The intricate regulation of chromatin plays a key role in controlling genome architecture and accessibility. Histone lysine methyltransferases regulate chromatin by catalyzing the methylation of specific histone residues but are also hypothesized to have equally important non-catalytic roles. SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation, and is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes suggesting the enzyme likely has uncharacterized non-catalytic activities. To characterize the catalytic and non-catalytic mechanisms SUV420H1 uses to modify chromatin, we determined cryo- EM structures of SUV420H1 complexes with nucleosomes containing histone H2A or its variant H2A.Z. Our structural, biochemical, biophysical, and cellular analyses reveal how both SUV420H1 recognizes its substrate and H2A.Z stimulates its activity, and show that SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from histone octamer. We hypothesize that this detachment increases DNA accessibility to large macromolecular complexes, a prerequisite for DNA replication and repair. We also show that SUV420H1 can promote chromatin condensates, another non-catalytic role that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.

Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination.

Genomic DNA is a crowded track where motor proteins frequently collide. It remains underexplored whether these collisions carry physiological function. In this work, we develop a single-molecule assay to visualize the trafficking of individual E. coli RNA polymerases (RNAPs) on DNA. Based on transcriptomic data, we hypothesize that RNAP collisions drive bidirectional transcription termination of convergent gene pairs. Single-molecule results show that the head-on collision between two converging RNAPs is necessary to prevent transcriptional readthrough but insufficient to release the RNAPs from the DNA. Remarkably, co-directional collision of a trailing RNAP into the head-on collided complex dramatically increases the termination efficiency. Furthermore, stem-loop structures formed in the nascent RNA are required for collisions to occur at well-defined positions between convergent genes. These findings suggest that physical collisions between RNAPs furnish a mechanism for transcription termination and that programmed genomic conflicts can be exploited to co-regulate the expression of multiple genes.

Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome.

Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis, an infectious disease that inflicts major health and economic costs around the world 1 . Mtb encounters a diversity of environments during its lifecycle, and responds to these changing environments by reprogramming its transcriptional output 2 . However, the transcriptomic features of Mtb remain poorly characterized. In this work, we comprehensively profile the Mtb transcriptome using the SEnd-seq method that simultaneously captures the 5' and 3' ends of RNA 3 . Surprisingly, we find that the RNA coverage for most of the Mtb transcription units display a gradual drop-off within a 200-500 nucleotide window downstream of the transcription start site, yielding a massive number of incomplete transcripts with heterogeneous 3' ends. We further show that the accumulation of these short RNAs is mainly due to the intrinsically low processivity of the Mtb transcription machinery rather than trans-acting factors such as Rho. Finally, we demonstrate that transcription-translation coupling plays a critical role in generating full-length protein-coding transcripts in Mtb. In sum, our results depict a mycobacterial transcriptome that is dominated by incomplete RNA products, suggesting a distinctive set of transcriptional regulatory mechanisms that could be exploited for new therapeutics.

High-Mobility Flexible Transistors with Low-Temperature Solution-Processed Tungsten Dichalcogenides.

The investigation of high-mobility two-dimensional (2D) flakes beyond molybdenum disulfide (MoS2) will be necessary to create a library of high-mobility solution-processed networks that conform to substrates and remain functional over thousands of bending cycles. Here we report electrochemical exfoliation of large-aspect-ratio (>100) semiconducting flakes of tungsten diselenide (WSe2) and tungsten disulfide (WS2) as well as MoS2 as a comparison. We use Langmuir-Schaefer coating to achieve highly aligned and conformal flake networks, with minimal mesoporosity (∼2-5%), at low processing temperatures (120 °C) and without acid treatments. This allows us to fabricate electrochemical transistors in ambient air, achieving average mobilities of µMoS2 ≈ 11 cm2 V-1 s-1, µWS2 ≈ 9 cm2 V-1 s-1, and µWSe2 ≈ 2 cm2 V-1 s-1 with a current on/off ratios of Ion/Ioff ≈ 2.6 × 103, 3.4 × 103, and 4.2 × 104 for MoS2, WS2, and WSe2, respectively. Moreover, our transistors display threshold voltages near ∼0.4 V with subthreshold slopes as low as 182 mV/dec, which are essential factors in maintaining power efficiency and represent a 1 order of magnitude improvement in the state of the art. Furthermore, the performance of our WSe2 transistors is maintained on polyethylene terephthalate (PET) even after 1000 bending cycles at 1% strain.

Structure and DNA bridging activity of the essential Rec114â€"Mei4 trimer interface.

The DNA double-strand breaks (DSBs) that initiate meiotic recombination are formed by an evolutionarily conserved suite of factors that includes Rec114 and Mei4 (RM), which regulate DSB formation both spatially and temporally. In vivo , these proteins form large immunostaining foci that are integrated with higher order chromosome structures. In vitro , they form a 2:1 heterotrimeric complex that binds cooperatively to DNA to form large, dynamic condensates. However, understanding of the atomic structures and dynamic DNA binding properties of RM complexes is lacking. Here, we report a structural model of a heterotrimeric complex of the C-terminus of Rec114 with the N-terminus of Mei4, supported by nuclear magnetic resonance experiments. This minimal complex, which lacks the predicted intrinsically disordered region of Rec114, is sufficient to bind DNA and form condensates. Single-molecule experiments reveal that the minimal complex can bridge two or more DNA duplexes and can generate force to condense DNA through long-range interactions. AlphaFold2 predicts similar structural models for RM orthologs across diverse taxa despite their low degree of sequence similarity. These findings provide insight into the conserved networks of protein-protein and protein-DNA interactions that enable condensate formation and promote formation of meiotic DSBs.