Dubs

Phages play an essential role in controlling bacterial populations. Those infecting Pelagibacterales (SAR11), the dominant bacteria in surface oceans, have been studied in silico and by cultivation attempts. However, little is known about the quantity of phage-infected cells in the environment. Using fluorescence in situ hybridization techniques, we here show pelagiphage-infected SAR11 cells across multiple global ecosystems and present evidence for tight community control of pelagiphages on the SAR11 hosts in a case study...

This article studies an emerging practical problem called heterogeneous prototype learning (HPL). Unlike the conventional heterogeneous face synthesis (HFS) problem that focuses on precisely translating a face image from a source domain to another target one without removing facial variations, HPL aims at learning the variation-free prototype of an image in the target domain while preserving the identity characteristics. HPL is a compounded problem involving two cross-coupled subproblems, that is, domain transfer and prototype learning (PL), thus making most of the existing HFS methods that simply transfer the domain style of images unsuitable for HPL...

Optical fibers aim to image in vivo biological processes. In this context, high spatial resolution and stability to fiber movements are key to enable decision-making processes (e.g. for microendoscopy). Recently, a single-pixel imaging technique based on a multicore fiber photonic lantern has been designed, named computational optical imaging using a lantern (COIL). A proximal algorithm based on a sparsity prior, dubbed SARA-COIL, has been further proposed to solve the associated inverse problem, to enable image reconstructions for high resolution COIL microendoscopy...

BACKGROUND: CDC6 is an oncogenic protein whose expression level fluctuates during the cell cycle. Although several E3 ubiquitin ligases responsible for the ubiquitin-mediated proteolysis of CDC6 have been identified, the deubiquitination pathway for CDC6 has not been investigated. METHODS: The proteome-wide deubiquitinase (DUB) screening was used to identify the potential regulator of CDC6. Immunofluorescence, protein half-life and deubiquitination assays were performed to determine the protein stability of CDC6...

Unknown image deformation and few-shot issues have posed significant challenges to inverse synthetic aperture radar (ISAR) target classification. To achieve robust feature representation and precise correlation modeling, this article proposes a novel two-stage few-shot ISAR classification network, dubbed as robust embedding and manifold inference (REMI). In the robust embedding stage, a multihead spatial transformation network (MH-STN) is designed to adjust unknown image deformations from multiple perspectives...

Leaf morphology plays a crucial role in plant classification and provides a significant model for studying plant diversity while directly impacting photosynthetic efficiency. In the case of melons, leaf shape not only influences production and classification but also represents a key genetic trait that requires further exploration. In this study, we utilized forward genetics to pinpoint a recessive locus, dubbed Cmrl ( Round leaf ), which is responsible for regulating melon leaf shape. Through bulked segregant analysis sequencing and extensive evaluation of a two-year F2 population, we successfully mapped the Cmrl locus to a 537...

Nanobodies have emerged as promising tools in biomedicine due to their single-chain structure and inherent stability. They generally have convex paratopes, which potentially prefer different epitope sites in an antigen compared to traditional antibodies. In this study, a synthetic phage display nanobody library was constructed and used to identify nanobodies targeting a tumor-associated antigen, the human B7-H3 protein. Combining next-generation sequencing and single-clone validation, two nanobodies were identified to specifically bind B7-H3 with medium nanomolar affinities...

Deubiquitinating enzyme A (DUBA), a member of the ovarian tumor (OTU) subfamily of deubiquitinases (DUBs), is recognized for its negative regulatory role in type I interferon (IFN) expression downstream of Toll-like receptor 3 (TLR3). However, its involvement in the TLR3 signaling pathway in fish remains largely unexplored. In this study, we investigated the regulatory role of DUBA (OmDUBA) in the TLR3 response in rainbow trout (Oncorhynchus mykiss). OmDUBA features a conserved OTU domain, and its expression increased in RTH-149 cells following stimulation with the TLR3 agonist poly(I:C)...

Many of the tissues/lesions in the medical images may be ambiguous. Therefore, medical segmentation is typically annotated by a group of clinical experts to mitigate personal bias. A common solution to fuse different annotations is the majority vote, e.g., taking the average of multiple labels. However, such a strategy ignores the difference between the grader expertness. Inspired by the observation that medical image segmentation is usually used to assist the disease diagnosis in clinical practice, we propose the diagnosis-first principle, which is to take disease diagnosis as the criterion to calibrate the inter-observer segmentation uncertainty...

Activation of the NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome complex is an essential innate immune signaling mechanism. To reveal how human NLRP3 inflammasome assembly and activation are controlled, in particular by components of the ubiquitin system, proximity labeling, affinity purification, and RNAi screening approaches were performed. Our study provides an intricate time-resolved molecular map of different phases of NLRP3 inflammasome activation. Also, we show that ubiquitin C-terminal hydrolase 1 (UCH-L1) interacts with the NACHT domain of NLRP3...

Linear response (LR) theory is a powerful tool in classic quantum chemistry crucial to understanding photoinduced processes in chemistry and biology. However, performing simulations for large systems and in the case of strong electron correlation remains challenging. Quantum computers are poised to facilitate the simulation of such systems, and recently, a quantum linear response formulation (qLR) was introduced [Kumar et al., J. Chem. Theory Comput. 2023 , 19 , 9136-9150]. To apply qLR to near-term quantum computers beyond a minimal basis set, we here introduce a resource-efficient qLR theory, using a truncated active-space version of the multiconfigurational self-consistent field LR ansatz...

MOTIVATION: Recent advancements in natural language processing have highlighted the effectiveness of global contextualized representations from Protein Language Models (pLMs) in numerous downstream tasks. Nonetheless, strategies to encode the site-of-interest leveraging pLMs for per-residue prediction tasks, such as crotonylation (Kcr) prediction, remain largely uncharted. RESULTS: Herein, we adopt a range of approaches for utilizing pLMs by experimenting with different input sequence types (full-length protein sequence versus window sequence), assessing the implications of utilizing per-residue embedding of the site-of-interest as well as embeddings of window residues centered around it...

BACKGROUND: Deubiquitinating enzymes (DUBs) cleave ubiquitin on substrate molecules to maintain protein stability. DUBs reportedly participate in the tumorigenesis and tumour progression of hepatocellular carcinoma (HCC). OTU deubiquitinase 5 (OTUD5), a DUB family member, has been recognized as a critical regulator in bladder cancer, breast cancer and HCC. However, the expression and biological function of OTUD5 in HCC are still controversial. RESULTS: We determined that the expression of OTUD5 was significantly upregulated in HCC tissues...

OBJECTIVE: To improve image quality in highly accelerated parameter mapping by incorporating a linear constraint that relates consecutive images. APPROACH: In multi-echo T1 or T2 mapping, scan time is often shortened by acquiring undersampled but complementary measures of k-space at each TE or TI. However, residual undersampling artifacts from the individual images can then degrade the quality of the final parameter maps. In this work, a new reconstruction method, dubbed Constrained Alternating Minimization for Parameter mapping (CAMP), is introduced...

Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, and deubiquitylating enzymes (DUBs) or erasers...

Diffuse cystic lung disease (DCLD) represents a heterogeneous group of conditions, typically characterized by the presence of multiple thin-walled, predominantly round parenchymal lucencies. The increased accessibility of computed tomography (CT) underscores the growing relevance of a relatively rare group of diseases as more clinicians are confronted with the presence of multiple lung cysts on the chest CT scan. Although the etiology of these conditions is very diverse, the focus of the differential diagnosis revolves around four primary causative factors - Lymphangioleiomyomatosis (LAM), Pulmonary Langerhanscell histiocytosis (PLCH), Birt-Hogg-Dubé (BHD) and lymphoid interstitial pneumonia (LIP)...

Despite its significant progress, cross-modal retrieval still suffers from one-to-many matching cases, where the multiplicity of semantic instances in another modality could be acquired by a given query. However, existing approaches usually map heterogeneous data into the learned space as deterministic point vectors. In spite of their remarkable performance in matching the most similar instance, such deterministic point embedding suffers from the insufficient representation of rich semantics in one-to-many correspondence...

Due to its wide application, deep reinforcement learning (DRL) has been extensively studied in the motion planning community in recent years. However, in the current DRL research, regardless of task completion, the state information of the agent will be reset afterward. This leads to a low sample utilization rate and hinders further explorations of the environment. Moreover, in the initial training stage, the agent has a weak learning ability in general, which affects the training efficiency in complex tasks...

INTRODUCTION: Articulography and functional neuroimaging are two major tools for studying the neurobiology of speech production. Until now, however, it has generally not been feasible to use both in the same experimental setup because of technical incompatibilities between the two methodologies. METHODS: Here we describe results from a novel articulography system dubbed Magneto-articulography for the Assessment of Speech Kinematics (MASK), which is technically compatible with magnetoencephalography (MEG) brain scanning systems...

Ubiquitin-specific protease 18 (USP18) is a multifunctional cysteine protease primarily responsible for deconjugating interferon-inducible ubiquitin-like (Ubl) modifier ISG15 from protein substrates. Here, we report the design and synthesis of activity-based probes (ABPs) capable of selectively detecting USP18 activity over other ISG15 cross-reactive deubiquitinases (DUBs) by incorporating unnatural amino acids into the C-terminal tail of ISG15. Combining with a ubiquitin-based DUB ABP, the selective USP18 ABP is employed in a chemoproteomic screening platform to identify and assess inhibitors of DUBs including USP18...