Oxidative balance score: a potential tool for reducing the risk of colorectal cancer and its subsites incidences.

Background: The Oxidative Balance Score (OBS) is commonly used to assess oxidative stress and provides a comprehensive evaluation of dietary and lifestyle-related exposures. However, there is limited research on the association between OBS and colorectal cancer (CRC), its subsites, and complications. The objective of this study was to assess the relationship between OBS and the risk of CRC, its subsites, and common complications in a large prospective cohort study. Methods: We included data from 175,808 participants in the UK Biobank data sample repository from 2006 to 2010. We evaluated OBS using a scoring system based on 22 dietary and lifestyle factors. Multiple adjustments, including multivariate Cox proportional hazard regression, gender stratification, subgroup analysis, and sensitivity analysis, were performed to fully explore the relationship between OBS and CRC, its subsites, and complications. The mediation analysis was conducted to investigate whether serum albumin, uric acid, and neutrophil levels mediate the relationship between OBS and CRC. Results: After adjusting for potential confounding factors, a significant negative correlation was found between OBS and the risk of CRC and its subsites (proximal colon cancer, distal colon cancer, and rectal cancer). This correlation was particularly pronounced in male CRC patients. Serum albumin, uric acid, and neutrophil count, which are biomarkers, were found to have a significant mediating effect between OBS and CRC. Conclusion: Our study suggests that higher exposure to antioxidants assessed through OBS (diet and lifestyle rich in antioxidants) may decrease the occurrence of CRC and its subsites.

Applications of gastric peroral endoscopic myotomy in the treatment of upper gastrointestinal tract disease.

Gastric peroral endoscopic myotomy (G-POME) is an emerging minimally invasive endoscopic technique involving the establishment of a submucosal tunnel around the pyloric sphincter. In 2013, Khashab et al used G-POME for the first time in the treatment of gastroparesis with enhanced therapeutic efficacy, providing a new direction for the treatment of gastroparesis. With the recent and rapid development of G-POME therapy technology, progress has been made in the treatment of gastroparesis and other upper digestive tract diseases, such as congenital hypertrophic pyloric stenosis and gastric sleeve stricture, with G-POME. This article reviews the research progress and future prospects of G-POME for the treatment of upper digestive tract gastrointestinal diseases.

Broad Spectrum Image Deblurring via an Adaptive Super-Network.

In blurry images, the degree of image blurs may vary drastically due to different factors, such as varying speeds of shaking cameras and moving objects, as well as defects of the camera lens. However, current end-to-end models failed to explicitly take into account such diversity of blurs. This unawareness compromises the specialization at each blur level, yielding sub-optimal deblurred images as well as redundant post-processing. Therefore, how to specialize one model simultaneously at different blur levels, while still ensuring coverage and generalization, becomes an emerging challenge. In this work, we propose Ada-Deblur, a super-network that can be applied to a "broad spectrum" of blur levels with no re-training on novel blurs. To balance between individual blur level specialization and wide-range blur levels coverage, the key idea is to dynamically adapt the network architectures from a single well-trained super-network structure, targeting flexible image processing with different deblurring capacities at test time. Extensive experiments demonstrate that our work outperforms strong baselines by demonstrating better reconstruction accuracy while incurring minimal computational overhead. Besides, we show that our method is effective for both synthetic and realistic blurs compared to these baselines. The performance gap between our model and the state-of-the-art becomes more prominent when testing with unseen and strong blur levels. Specifically, our model demonstrates surprising deblurring performance on these images with PSNR improvements of around 1 dB. Our code is publicly available at https://github.com/wuqiuche/Ada-Deblur.

Visualizing Cathepsin K-Cre Expression at the Single-Cell Level with GFP Reporters.

The Cre/lox system is a fundamental tool for functional genomic studies, and a number of Cre lines have been generated to target genes of interest spatially and temporally in defined cells or tissues; this approach has greatly expanded our knowledge of gene functions. However, the limitations of this system have recently been recognized, and we must address the challenge of so-called nonspecific/off-target effects when a Cre line is utilized to investigate a gene of interest. For example, cathepsin K (Ctsk) has been used as a specific osteoclast marker, and Cre driven by its promoter is widely utilized for osteoclast investigations. However, Ctsk-Cre expression has recently been identified in other cell types, such as osteocytes, periosteal stem cells, and tenocytes. To better understand Ctsk-Cre expression and ensure appropriate use of this Cre line, we performed a comprehensive analysis of Ctsk-Cre expression at the single-cell level in major organs and tissues using two green fluorescent protein (GFP) reporters (ROSA nT-nG and ROSA tdT) and a tissue clearing technique in young and aging mice. The expression profile was further verified by immunofluorescence staining and droplet digital RT-PCR. The results demonstrate that Ctsk-Cre is expressed not only in osteoclasts but also at various levels in osteoblast lineage cells and other major organs/tissues, particularly in the brain, kidney, pancreas, and blood vessels. Furthermore, Ctsk-Cre expression increases markedly in the bone marrow, skeletal muscle, and intervertebral discs in aging mice. These data will be valuable for accurately interpreting data obtained from in vivo studies using Ctsk-Cre mice to avoid potentially misleading conclusions. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Exploring the intestinal ecosystem: from gut microbiota to associations with subtypes of inflammatory bowel disease.

Objective: Significant differences have been discovered between subtypes of Crohn's disease (CD) and ulcerative colitis (UC). The role of gut microbiota in promoting the onset of UC and CD is established, but conclusions regarding subtype-specific analyses remain limited. Methods: This study aims to explore the influence of gut microbiota on subtypes of UC and CD, offering novel insights into the pathogenesis and treatment of UC and CD.Two-sample Mendelian randomization (MR) analysis was employed to examine the causal relationship between subtypes of UC and CD and gut microbiota composition. Gut microbiota data were sourced from the International Consortium MiBioGen, while UC and CD data were obtained from FINNGEN. Eligible single nucleotide polymorphisms (SNPs) were selected as instrumental variables. Multiple analytical approaches such as inverse variance-weighted (IVW), MR-Egger regression, weighted median, weighted mode, and MR-RAPS were utilized. Sensitivity analyses including MR-Egger intercept test, Cochran's Q test, and leave-one-out analysis were conducted for quality control. Subsequently, we employed multivariable IVW, MR-Egger, weighted median, and LASSO regression methods to identify independently significant genera or families and conducted sensitivity analyses. Results: We have determined that Hungatella, Acidaminococcaceae, and 15 other microbial taxa act as protective factors for various CD and UC subtypes, while Terrisporobacter, Anaerostipes, and 23 other microbial taxa are associated with increased risk for different CD and UC subtypes. Furthermore, through multivariable MR analysis, we have identified significant genera or families with independent effects. Conclusion: Our study confirms a causal relationship between dysbiosis of gut microbiota and the occurrence of CD and UC subtypes. Furthermore, it validates etiological distinctions among different subtypes of CD and UC. A novel approach to adjunctive therapy involving distinct UC or CD subtypes may involve the use of probiotics and represents a potential avenue for future treatments.

Domain Generalization for Language-Independent Automatic Speech Recognition.

A language-independent automatic speech recognizer (ASR) is one that can be used for phonetic transcription in languages other than the languages in which it was trained. Language-independent ASR is difficult to train, because different languages implement phones differently: even when phonemes in two different languages are written using the same symbols in the international phonetic alphabet, they are differentiated by different distributions of language-dependent redundant articulatory features. This article demonstrates that the goal of language-independence may be approximated in different ways, depending on the size of the training set, the presence vs. absence of familial relationships between the training and test languages, and the method used to implement phone recognition or classification. When the training set contains many languages, and when every language in the test set is related (shares the same language family with) a language in the training set, then language-independent ASR may be trained using an empirical risk minimization strategy (e.g., using connectionist temporal classification without extra regularizers). When the training set is limited to a small number of languages from one language family, however, and the test languages are not from the same language family, then the best performance is achieved by using domain-invariant representation learning strategies. Two different representation learning strategies are tested in this article: invariant risk minimization, and regret minimization. We find that invariant risk minimization is better at the task of phone token classification (given known segment boundary times), while regret minimization is better at the task of phone token recognition.

Learning Temporal Dynamics for Video Super-Resolution: A Deep Learning Approach.

Video super-resolution (SR) aims at estimating a high-resolution (HR) video sequence from a low-resolution (LR) one. Given that deep learning has been successfully applied to the task of single image SR, which demonstrates the strong capability of neural networks for modeling spatial relation within one single image, the key challenge to conduct video SR is how to efficiently and effectively exploit the temporal dependency among consecutive LR frames other than the spatial relation. However, this remains challenging because complex motion is difficult to model and can bring detrimental effects if not handled properly. We tackle the problem of learning temporal dynamics from two aspects. First, we propose a temporal adaptive neural network that can adaptively determine the optimal scale of temporal dependency. Inspired by the Inception module in GoogLeNet [1], filters of various temporal scales are applied to the input LR sequence before their responses are adaptively aggregated, in order to fully exploit the temporal relation among consecutive LR frames. Second, we decrease the complexity of motion among neighboring frames using a spatial alignment network that can be end-to-end trained with the temporal adaptive network and has the merit of increasing the robustness to complex motion and the efficiency compared to competing image alignment methods. We provide a comprehensive evaluation of the temporal adaptation and the spatial alignment modules. We show the temporal adaptive design considerably improve SR quality over its plain counterparts, and the spatial alignment network is able to attain comparable SR performance with the sophisticated optical flow based approach, but requires much less running time. Overall our proposed model with learned temporal dynamics is shown to achieve state-of-the-art SR results in terms of not only spatial consistency but also temporal coherence on public video datasets. More information can be found in.

Greedy Batch-Based Minimum-Cost Flows for Tracking Multiple Objects.

Minimum-cost flow algorithms have recently achieved state-of-the-art results in multi-object tracking. However, they rely on the whole image sequence as input. When deployed in real-time applications or in distributed settings, these algorithms first operate on short batches of frames and then stitch the results into full trajectories. This decoupled strategy is prone to errors because the batch-based tracking errors may propagate to the final trajectories and cannot be corrected by other batches. In this paper, we propose a greedy batch-based minimum-cost flow approach for tracking multiple objects. Unlike existing approaches that conduct batch-based tracking and stitching sequentially, we optimize consecutive batches jointly so that the tracking results on one batch may benefit the results on the other. Specifically, we apply a generalized minimum-cost flows (MCF) algorithm on each batch and generate a set of conflicting trajectories. These trajectories comprise the ones with high probabilities, but also those with low probabilities potentially missed by detectors and trackers. We then apply the generalized MCF again to obtain the optimal matching between trajectories from consecutive batches. Our proposed approach is simple, effective, and does not require training. We demonstrate the power of our approach on data sets of different scenarios.

Unsupervised Sequential Outlier Detection With Deep Architectures.

Unsupervised outlier detection is a vital task and has high impact on a wide variety of applications domains, such as image analysis and video surveillance. It also gains long-standing attentions and has been extensively studied in multiple research areas. Detecting and taking action on outliers as quickly as possible are imperative in order to protect network and related stakeholders or to maintain the reliability of critical systems. However, outlier detection is difficult due to the one class nature and challenges in feature construction. Sequential anomaly detection is even harder with more challenges from temporal correlation in data, as well as the presence of noise and high dimensionality. In this paper, we introduce a novel deep structured framework to solve the challenging sequential outlier detection problem. We use autoencoder models to capture the intrinsic difference between outliers and normal instances and integrate the models to recurrent neural networks that allow the learning to make use of previous context as well as make the learners more robust to warp along the time axis. Furthermore, we propose to use a layerwise training procedure, which significantly simplifies the training procedure and hence helps achieve efficient and scalable training. In addition, we investigate a fine-tuning step to update all parameters set by incorporating the temporal correlation in the sequence. We further apply our proposed models to conduct systematic experiments on five real-world benchmark data sets. Experimental results demonstrate the effectiveness of our model, compared with other state-of-the-art approaches.

Learning Super-Resolution Jointly From External and Internal Examples.

Single image super-resolution (SR) aims to estimate a high-resolution (HR) image from a low-resolution (LR) input. Image priors are commonly learned to regularize the, otherwise, seriously ill-posed SR problem, either using external LR-HR pairs or internal similar patterns. We propose joint SR to adaptively combine the advantages of both external and internal SR methods. We define two loss functions using sparse coding-based external examples, and epitomic matching based on internal examples, as well as a corresponding adaptive weight to automatically balance their contributions according to their reconstruction errors. Extensive SR results demonstrate the effectiveness of the proposed method over the existing state-of-the-art methods, and is also verified by our subjective evaluation study.

Blind image deblurring using spectral properties of convolution operators.

Blind deconvolution is to recover a sharp version of a given blurry image or signal when the blur kernel is unknown. Because this problem is ill-conditioned in nature, effectual criteria pertaining to both the sharp image and blur kernel are required to constrain the space of candidate solutions. While the problem has been extensively studied for long, it is still unclear how to regularize the blur kernel in an elegant, effective fashion. In this paper, we show that the blurry image itself actually encodes rich information about the blur kernel, and such information can indeed be found by exploring and utilizing a well-known phenomenon, that is, sharp images are often high pass, whereas blurry images are usually low pass. More precisely, we shall show that the blur kernel can be retrieved through analyzing and comparing how the spectrum of an image as a convolution operator changes before and after blurring. Subsequently, we establish a convex kernel regularizer, which depends only on the given blurry image. Interestingly, the minimizer of this regularizer guarantees to give a good estimate to the desired blur kernel if the original image is sharp enough. By combining this powerful regularizer with the prevalent nonblind devonvolution techniques, we show how we could significantly improve the deblurring results through simulations on synthetic images and experiments on realistic images.

The fragment transformation method to detect the protein structural motifs.

To identify functional structural motifs from protein structures of unknown function becomes increasingly important in recent years due to the progress of the structural genomics initiatives. Although certain structural patterns such as the Asp-His-Ser catalytic triad are easy to detect because of their conserved residues and stringently constrained geometry, it is usually more challenging to detect a general structural motifs like, for example, the betabetaalpha-metal binding motif, which has a much more variable conformation and sequence. At present, the identification of these motifs usually relies on manual procedures based on different structure and sequence analysis tools. In this study, we develop a structural alignment algorithm combining both structural and sequence information to identify the local structure motifs. We applied our method to the following examples: the betabetaalpha-metal binding motif and the treble clef motif. The betabetaalpha-metal binding motif plays an important role in nonspecific DNA interactions and cleavage in host defense and apoptosis. The treble clef motif is a zinc-binding motif adaptable to diverse functions such as the binding of nucleic acid and hydrolysis of phosphodiester bonds. Our results are encouraging, indicating that we can effectively identify these structural motifs in an automatic fashion. Our method may provide a useful means for automatic functional annotation through detecting structural motifs associated with particular functions.