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In this paper, we analyze and discuss ShadowFormer in preparation for the NTIRE2023 Shadow Removal Challenge [1], implementing five key improvements: image alignment, the introduction of a perceptual quality loss function, the semi-automatic annotation for shadow detection, joint learning of shadow detection and removal, and the introduction of new data augmentation technique "CutShadow" for shadow removal. Our method achieved scores of 0.196 (3rd out of 19) in LPIPS and 7.44 (4th out of 19) in the Mean Opinion Score (MOS)., Comment: This version is a brief technical report submitted to the organizers, and there are still some points to be added; please wait for updates until May 2024. The code can be found here (https://github.com/Yuki-11/NTIRE2023_ShadowRemoval_IIM_TTI)

Continuous, rather than discrete, data on animal population are ideal for identifying the causal relationships driving population fluctuations. In this study, we reveal the effect of forest regeneration after logging on the habitat, food availability, and abundance of Japanese macaques over two decades, spanning the period from 2000 until 2019, based on a continuous population census conducted every year. Three vegetation types, covering an area of 7.5 km², make up our study sites: primary forests, forests logged from 1984 until 1995 and then naturally regenerated (natural regeneration), and forests logged from 1975 until 1983 and then planted with cedars (plantation). In natural regeneration, both individual and total tree biomass increased, in particular naturally grown cedars. In plantation, the number of trees decreased and the total biomass did not change, mainly due to thinning (partial removal of planted cedars to harvest timber) in 2015. A state space model suggests that the relative fruit production in natural regeneration to that in the primary forest tended to be low after 2012, a condition brought about by cleaning cutting to remove non-cedar broad-leaved trees and shrubs in natural regeneration. An analysis of aerial photos detected an increase in naturally grown cedar patches in natural regeneration between 2009 and 2014. We also observed a population decrease of Japanese macaques in natural regeneration but not in primary and plantation forests. The state space model indicates that this decrease occurred in the first half of the study period, which was earlier than the replacement of cedar patches in natural regeneration. The high time resolution of our data refutes the simple scenario that macaques decreased their number in natural regeneration due to the reduced food availability there. The less frequent use of natural regeneration began as a stochastic event; i.e., the disappearance of multiple individuals from a group ranging there, and then the s

Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution.

This paper proposes crack segmentation augmented by super resolution (SR) with deep neural networks. In the proposed method, a SR network is jointly trained with a binary segmentation network in an end-to-end manner. This joint learning allows the SR network to be optimized for improving segmentation results. For realistic scenarios, the SR network is extended from non-blind to blind for processing a low-resolution image degraded by unknown blurs. The joint network is improved by our proposed two extra paths that further encourage the mutual optimization between SR and segmentation. Comparative experiments with State of The Art (SoTA) segmentation methods demonstrate the superiority of our joint learning, and various ablation studies prove the effects of our contributions., Comment: Accepted to IEEE Transactions on Instrumentation and Measurement (TIM) 2024. The project page is located at https://yuki-11.github.io/CSBSR-project-page

Since non-blind Super Resolution (SR) fails to super-resolve Low-Resolution (LR) images degraded by arbitrary degradations, SR with the degradation model is required. However, this paper reveals that non-blind SR that is trained simply with various blur kernels exhibits comparable performance as those with the degradation model for blind SR. This result motivates us to revisit high-performance non-blind SR and extend it to blind SR with blur kernels. This paper proposes two SR networks by integrating kernel estimation and SR branches in an iterative end-to-end manner. In the first model, which is called the Kernel Conditioned Back-Projection Network (KCBPN), the low-dimensional kernel representations are estimated for conditioning the SR branch. In our second model, the Kernelized BackProjection Network (KBPN), a raw kernel is estimated and directly employed for modeling the image degradation. The estimated kernel is employed not only for back-propagating its residual but also for forward-propagating the residual to iterative stages. This forward-propagation encourages these stages to learn a variety of different features in different stages by focusing on pixels with large residuals in each stage. Experimental results validate the effectiveness of our proposed networks for kernel estimation and SR. We will release the code for this work., Comment: The first two authors contributed equally to this work

Small Object Detection (SOD) is an important machine vision topic because (i) a variety of real-world applications require object detection for distant objects and (ii) SOD is a challenging task due to the noisy, blurred, and less-informative image appearances of small objects. This paper proposes a new SOD dataset consisting of 39,070 images including 137,121 bird instances, which is called the Small Object Detection for Spotting Birds (SOD4SB) dataset. The detail of the challenge with the SOD4SB dataset is introduced in this paper. In total, 223 participants joined this challenge. This paper briefly introduces the award-winning methods. The dataset, the baseline code, and the website for evaluation on the public testset are publicly available., Comment: This paper is included in the proceedings of the 18th International Conference on Machine Vision Applications (MVA2023). It will be officially published at a later date. Project page : https://www.mva-org.jp/mva2023/challenge

Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution., identifier:2211-1247

Nudix hydrolase (NUDX) hydrolyzes 8-oxo-(d)GTP to reduce the levels of oxidized nucleotides in the cells. 8-oxo-(d)GTP produced by reactive oxygen species (ROS) is incorporated into DNA/RNA and mispaired with adenine, causing replicational and transcriptional errors. Here, we identified a rice OsNUDX2 gene, whose expression level was increased 15-fold under UV-C irradiation. The open reading frame of the OsNUDX2 gene, which encodes 776 amino acid residues, was cloned into Escherichia coli cells to produce the protein of 100 kDa. The recombinant protein hydrolyzed 8-oxo-dGTP, in addition to dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP), as did Arabidopsis AtNUDX1; whereas the amino acid sequence of OsNUDX2 had 18% identity with AtNUDX1. OsNUDX2 had 14% identity with barley HvNUDX12, which hydrolyzes 8-oxo-dGTP and diadenosine tetraphosphates. Suppression of the lacZ amber mutation caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree when the OsNUDX2 gene was expressed in mutT-deficient E. coli cells. These results suggest that the different substrate specificity and identity among plant 8-oxo-dGTP-hydrolyzing NUDXs and OsNUDX2 reduces UV stress by sanitizing the oxidized nucleotides.

Nudix hydrolase (NUDX) hydrolyzes 8-oxo-(d)GTP to reduce the levels of oxidized nucleotides in the cells. 8-oxo-(d)GTP produced by reactive oxygen species (ROS) is incorporated into DNA/RNA and mispaired with adenine, causing replicational and transcriptional errors. Here, we identified a rice OsNUDX2 gene, whose expression level was increased 15-fold under UV-C irradiation. The open reading frame of the OsNUDX2 gene, which encodes 776 amino acid residues, was cloned into Escherichia coli cells to produce the protein of 100 kDa. The recombinant protein hydrolyzed 8-oxo-dGTP, in addition to dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP), as did Arabidopsis AtNUDX1; whereas the amino acid sequence of OsNUDX2 had 18% identity with AtNUDX1. OsNUDX2 had 14% identity with barley HvNUDX12, which hydrolyzes 8-oxo-dGTP and diadenosine tetraphosphates. Suppression of the lacZ amber mutation caused by the incorporation of 8-oxo-GTP into mRNA was prevented to a significant degree when the OsNUDX2 gene was expressed in mutT-deficient E. coli cells. These results suggest that the different substrate specificity and identity among plant 8-oxo-dGTP-hydrolyzing NUDXs and OsNUDX2 reduces UV stress by sanitizing the oxidized nucleotides.

Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution.

Burst super-resolution has received increased attention in recent years due to its applications in mobile photography. By merging information from multiple shifted images of a scene, burst super-resolution aims to recover details which otherwise cannot be obtained using a simple input image. This paper reviews the NTIRE 2022 challenge on burst super-resolution. In the challenge, the participants were tasked with generating a clean RGB image with 4x higher resolution, given a RAW noisy burst as input. That is, the methods need to perform joint denoising, demosaicking, and super-resolution. The challenge consisted of 2 tracks. Track 1 employed synthetic data, where pixel-accurate high-resolution ground truths are available. Track 2 on the other hand used real-world bursts captured from a handheld camera, along with approximately aligned reference images captured using a DSLR. 14 teams participated in the final testing phase. The top performing methods establish a new state-of-the-art on the burst super-resolution task., Funding Agencies|Huawei; Reality Labs; Bending Spoons; MediaTek; OPPO; Oddity; Voyage81; ETH Zurich (Computer Vision Lab); University of Wurzburg (CAIDAS)

Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution., journal article

[Background] Visceral fat obesity can be defined quantitatively by abdominal computed tomography, however, the usefulness of measuring visceral fat area to assess the etiology of gastrointestinal reflux disease has not been fully elucidated. [Methods] A total of 433 healthy subjects aged 40–69 years (234 men, 199 women) were included in the study. The relationship between obesity-related factors (total fat area, visceral fat area, subcutaneous fat area, waist circumference, and body mass index) and the incidence of reflux erosive esophagitis was investigated. Lifestyle factors and stomach conditions relevant to the onset of erosive esophagitis were also analyzed. [Results] The prevalence of reflux erosive esophagitis was 27.2% (118/433; 106 men, 12 women). Visceral fat area was higher in subjects with erosive esophagitis than in those without (116.6 cm2 vs. 64.9 cm2, respectively). The incidence of erosive esophagitis was higher in subjects with visceral fat obesity (visceral fat area ≥ 100 cm2) than in those without (61.2% vs. 12.8%, respectively). Visceral fat obesity had the highest odds ratio (OR) among obesity-related factors. Multivariate analysis showed that visceral fat area was associated with the incidence of erosive esophagitis (OR = 2.18), indicating that it is an independent risk factor for erosive esophagitis. In addition, daily alcohol intake (OR = 1.54), gastric atrophy open type (OR = 0.29), and never-smoking history (OR = 0.49) were also independently associated with the development of erosive esophagitis. [Conclusions] Visceral fat obesity is the key risk factor for the development of reflux erosive esophagitis in subjects aged 40–69 years.

Radiotherapy (RT) is the primary treatment for cancer. Ionizing radiation from RT induces tumor damage at the irradiated site, and, although clinically infrequent, may cause regression of tumors distant from the irradiated site-a phenomenon known as the abscopal effect. Recently, the abscopal effect has been related to prolongation of overall survival time in cancer patients, though the factors that influence the abscopal effect are not well understood. The aim of this study is to clarify the factors influencing on abscopal effect. Here, we established a mouse model in which we induced the abscopal effect. We injected MC38 (mouse colon adenocarcinoma) cells subcutaneously into C57BL/6 mice at two sites. Only one tumor was irradiated and the sizes of both tumors were measured over time. The non-irradiated-site tumor showed regression, demonstrating the abscopal effect. This effect was enhanced by an increase in the irradiated-tumor volume and by administration of anti-PD1 antibody. When the abscopal effect was induced by a combination of RT and anti-PD1 antibody, it was also influenced by radiation dose and irradiated-tumor volume. These phenomena were also verified in other cell line, B16F10 cells (mouse melanoma cells). These findings provide further evidence of the mechanism for, and factors that influence, the abscopal effect in RT.

The phloem transports photosynthetic assimilates and signalling molecules. It mainly consists of sieve elements (SEs), which act as “highways” for transport, and companion cells (CCs), which serve as “gates” to load/unload cargos. Though SEs and CCs function together, it remains unknown what determines the ratio of SE/CC in the phloem. Here we develop a new culture system for CC differentiation in Arabidopsis named VISUAL-CC, which almost mimics the process of the SE–CC complex formation. Comparative expression analysis in VISUAL-CC reveals that SE and CC differentiation tends to show negative correlation, while total phloem differentiation is unchanged. This varying SE/CC ratio is largely dependent on GSK3 kinase activity. Indeed, gsk3 hextuple mutants possess many more SEs and fewer CCs, whereas gsk3 gain-of-function mutants partially increase the CC number. Taken together, GSK3 activity appears to function as a cell-fate switch in the phloem, thereby balancing the SE/CC ratio.

The phloem transports photosynthetic assimilates and signalling molecules. It mainly consists of sieve elements (SEs), which act as “highways” for transport, and companion cells (CCs), which serve as “gates” to load/unload cargos. Though SEs and CCs function together, it remains unknown what determines the ratio of SE/CC in the phloem. Here we develop a new culture system for CC differentiation in Arabidopsis named VISUAL-CC, which almost mimics the process of the SE–CC complex formation. Comparative expression analysis in VISUAL-CC reveals that SE and CC differentiation tends to show negative correlation, while total phloem differentiation is unchanged. This varying SE/CC ratio is largely dependent on GSK3 kinase activity. Indeed, gsk3 hextuple mutants possess many more SEs and fewer CCs, whereas gsk3 gain-of-function mutants partially increase the CC number. Taken together, GSK3 activity appears to function as a cell-fate switch in the phloem, thereby balancing the SE/CC ratio.

The development of an efficient and cost‐effective method for monitoring animal populations or biodiversity is urgently needed, and invertebrate‐derived DNA (iDNA) may offer a promising tool for assessing the diversity and other ecological information of vertebrates. We studied the host species of a hematophagous leech (Haemadipsa japonica) in Yakushima by genetic barcoding and compared the results with those for mammal composition revealed by camera trapping. We analyzed 119 samples using two sets of primers by Sanger sequencing and one set of primer by next generation sequencing. The proportion of the samples that were successfully sequenced and identified to at least one species was 11.8–24.3%, depending on the three different methods. In all of these three methods, most of the samples were identified as sika deer (18/20, 6/15 and 16/29) or human (2/20, 7/15 and 21/29). The nonhuman mammal host species composition was significantly different from that estimated by camera trapping. Sika deer was the main host, which may be related with their high abundance, large body size and terrestriality. Ten samples included DNA derived from multiple species of vertebrates. This may be due to the contamination of human DNA, but we also found DNA from deer, Japanese macaque and a frog in the same samples, suggesting the mixture of the two meals in the gut of the leech. Using H. japonica‐derived iDNA would not be suitable to make an inventory of species, but it may be useful to collect genetic information on the targeted species, due to their high host selectivity.

We can extract useful information from social media data by adding the user's home location. However, since the user's home location is generally not publicly available, many researchers have been attempting to develop a more accurate home location estimation. In this study, we propose a method to estimate a Twitter user's home location by using weather observation data from AMeDAS. In our method, we first estimate the weather of the area posted by an estimation target user by using the tweet, Next, we check out the estimated weather against weather observation data, and narrow down the area posted by the user. Finally, the user's home location is estimated as which areas the user frequently posts from. In our experiments, the results indicate that our method functions effectively and also demonstrate that accuracy improves under certain conditions., Comment: The 2017 International Conference On Advanced Informatics: Concepts, Theory And Application (ICAICTA2017)

We have investigated the wavelength dependence of the photoreduction of Ag+ ions in glass irradiated by visible femtosecond pulses. These pulses, issued at wavelengths ranging from 400 to 800 nm, were nonresonant with the glass absorption. In this article, a relationship between threshold powers, wavelengths, and linear and nonlinear refractive indices is described. The nonlinear refractive index of Ag+-doped glass was measured by an optical Kerr shutter method. The wavelength dependence of threshold powers of the photoreduction is explained by considering linear and nonlinear refractive indices. The mechanism of the photoreduction is also discussed.

We have investigated the wavelength dependence of the photoreduction of Ag+ ions in glass irradiated by visible femtosecond pulses. These pulses, issued at wavelengths ranging from 400 to 800 nm, were nonresonant with the glass absorption. In this article, a relationship between threshold powers, wavelengths, and linear and nonlinear refractive indices is described. The nonlinear refractive index of Ag+-doped glass was measured by an optical Kerr shutter method. The wavelength dependence of threshold powers of the photoreduction is explained by considering linear and nonlinear refractive indices. The mechanism of the photoreduction is also discussed.