Deformable Graph Transformer

Transformer-based models have recently shown success in representation learning on graph-structured data beyond natural language processing and computer vision. However, the success is limited to small-scale graphs due to the drawbacks of full dot-product attention on graphs such as the quadratic complexity with respect to the number of nodes and message aggregation from enormous irrelevant nodes. To address these issues, we propose Deformable Graph Transformer (DGT) that performs sparse attention via dynamically sampled relevant nodes for efficiently handling large-scale graphs with a linear complexity in the number of nodes. Specifically, our framework first constructs multiple node sequences with various criteria to consider both structural and semantic proximity. Then, combining with our learnable Katz Positional Encodings, the sparse attention is applied to the node sequences for learning node representations with a significantly reduced computational cost. Extensive experiments demonstrate that our DGT achieves state-of-the-art performance on 7 graph benchmark datasets with 2.5 - 449 times less computational cost compared to transformer-based graph models with full attention.Comment: 16 pages, 3 figure

IL-15 promotes self-renewal of progenitor exhausted CD8 T cells during persistent antigenic stimulation

In chronic infections and cancer, exhausted CD8 T cells exhibit heterogeneous subpopulations. TCF1+PD-1+ progenitor exhausted CD8 T cells (Tpex) can self-renew and give rise to Tim-3+PD-1+ terminally differentiated CD8 T cells that retain their effector functions. Tpex cells are thus essential to maintaining a pool of antigen-specific CD8 T cells during persistent antigenic stimulation, and only they respond to PD-1-targeted therapy. Despite their potential as a crucial therapeutic target for immune interventions, the mechanisms controlling the maintenance of virus-specific Tpex cells remain to be determined. We observed approximately 10-fold fewer Tpex cells in the spleens of mice chronically infected with lymphocytic choriomeningitis virus (LCMV) one-year post-infection (p.i.) than at three months p.i. Similar to memory CD8 T cells, Tpex cells have been found to undergo self-renewal in the lymphoid organs, prominently the bone marrow, during chronic LCMV infection. Furthermore, ex vivo treatment with IL-15 preferentially induced the proliferation of Tpex cells rather than the terminally differentiated subsets. Interestingly, single-cell RNA sequencing analysis of LCMV-specific exhausted CD8 T cells after ex vivo IL-15 treatment compared with those before treatment revealed increased expression of ribosome-related genes and decreased expression of genes associated with the TCR signaling pathway and apoptosis in both Tpex and Ttex subsets. The exogenous administration of IL-15 to chronically LCMV-infected mice also significantly increased self-renewal of Tpex cells in the spleen and bone marrow. In addition, we assessed the responsiveness of CD8 tumor-infiltrating lymphocytes (TILs) from renal cell carcinoma patients to IL-15. Similar to the data we obtained from chronic viral infection in mice, the expansion of the Tpex subset of PD-1+ CD8 TILs upon ex vivo IL-15 treatment was significantly higher than that of the terminally differentiated subset. These results show that IL-15 could promote self-renewal of Tpex cells, which has important therapeutic implications

An HR-MAS MR Metabolomics Study on Breast Tissues Obtained with Core Needle Biopsy

BACKGROUND: Much research has been devoted to the development of new breast cancer diagnostic measures, including those involving high-resolution magic angle spinning (HR-MAS) magnetic resonance (MR) spectroscopic techniques. Previous HR-MAS MR results have been obtained from post-surgery samples, which limits their direct clinical applicability. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we performed HR-MAS MR spectroscopic studies on 31 breast tissue samples (13 cancer and 18 non-cancer) obtained by percutaneous core needle biopsy. We showed that cancer and non-cancer samples can be discriminated very well with Orthogonal Projections to Latent Structure-Discriminant Analysis (OPLS-DA) multivariate model on the MR spectra. A subsequent blind test showed 69% sensitivity and 94% specificity in the prediction of the cancer status. A spectral analysis showed that in cancer cells, taurine- and choline-containing compounds are elevated. Our approach, additionally, could predict the progesterone receptor statuses of the cancer patients. CONCLUSIONS/SIGNIFICANCE: HR-MAS MR metabolomics on intact breast tissues obtained by core needle biopsy may have a potential to be used as a complement to the current diagnostic and prognostic measures for breast cancers

The Impact of Social Jetlag on Sleep Quality among Nurses: A Cross-Sectional Survey

Social jetlag (SJL) refers to an asynchrony between one’s chronotype and social working hours, which can be detrimental to health. The current SJL situation in shift nurses who work in dysregulation is poorly understood. Therefore, this study aimed to investigate SJL during night shifts and identify the predictors of sleep quality in rotating shift nurses. A cross-sectional study was conducted in 2018 on a sample of 132 shift-working nurses from two general hospitals in South Korea (the response rate was 88.8%). The SJL was measured with the Munich Chronotype Questionnaire, and sleep quality was measured with the Pittsburgh Sleep Quality Index and the Verran and Snyder–Halpern Sleep Scale. Data analysis was mainly based on a multiple regression, to identify SJL’s influence on nurses’ sleep quality. The average SJL during night shifts was 2 h and 3 min, and the average sleep duration during night shifts was 6 h 10 min. Multiple regression analysis revealed that SJL, day-shift fatigue, and sleep quality during night shifts affected nurses’ sleep quality. These variables accounted for 24.7% of the variance in overall sleep quality. The study concluded that overall sleep quality can increase with decreasing day-shift fatigue, decreasing SJL, and increasing sleep quality on night shifts

Epigenomic Analysis of RAD51 ChIP-seq Data Reveals cis-regulatory Elements Associated with Autophagy in Cancer Cell Lines

RAD51 is a recombinase that plays a pivotal role in homologous recombination. Although the role of RAD51 in homologous recombination has been extensively studied, it is unclear whether RAD51 can be involved in gene regulation as a co-factor. In this study, we found evidence that RAD51 may contribute to the regulation of genes involved in the autophagy pathway with E-box proteins such as USF1, USF2, and/or MITF in GM12878, HepG2, K562, and MCF-7 cell lines. The canonical USF binding motif (CACGTG) was significantly identified at RAD51-bound cis-regulatory elements in all four cell lines. In addition, genome-wide USF1, USF2, and/or MITF-binding regions significantly coincided with the RAD51-associated cis-regulatory elements in the same cell line. Interestingly, the promoters of genes associated with the autophagy pathway, such as ATG3 and ATG5, were significantly occupied by RAD51 and regulated by RAD51 in HepG2 and MCF-7 cell lines. Taken together, these results unveiled a novel role of RAD51 and provided evidence that RAD51-associated cis-regulatory elements could possibly be involved in regulating autophagy-related genes with E-box binding proteins

Fat-suppressed T-2 mapping of femoral cartilage in the porcine knee joint: A comparison with conventional T-2 mapping

PurposeTo investigate the effect of fat suppression on T-2 mapping of the articular cartilage in the porcine knee joint using magnetic resonance imaging (MRI). Materials and MethodsEleven porcine knee joints were harvested en bloc with intact capsules. We performed T-2 mapping of the articular cartilage in the medial femoral condyle at 3T either with (fat-suppressed T-2 mapping) or without (conventional T-2 mapping) fat suppression in the sagittal plane under two frequency-encoding directions: from superior to inferior (SI) and inferior to superior (IS). Two observers measured the T-2 values of the medial femoral condyle cartilage in four regions: in the anterior oblique, central horizontal, posterior oblique, and posterior vertical portions. We evaluated reproducibility of the fat-suppressed and conventional T-2 mapping by changing the frequency-encoding direction. ResultsThe mean T-2 values of fat-suppressed T-2 mapping were significantly lower than those of conventional T-2 mapping for five of eight comparisons (P < 0.017). The mean T-2 values between fat-suppressed T-2-SI and fat-suppressed T-2-IS did not differ significantly in any region (P=0.077-0.873). However, the mean T-2 values of conventional T-2-SI were significantly lower compared with conventional T-2-IS in three of the regions (P < 0.05). The intraclass correlation coefficient (ICC) between the two fat-suppressed T-2 maps was higher than the ICC between the two conventional T-2 maps (0.276-0.800 vs. -0.032-0.455) for three regions. ConclusionCompared with conventional T-2 mapping, fat-suppressed T-2 mapping provides lower T-2 values of the articular cartilage and more reproducible results for the porcine knee joint.N

Tailoring the Morphology of Supraparticles by Primary Colloids with Different Shapes, Sizes and Dispersities

Surface-templated evaporation driven (STED) method is a promising method to fabricate supraparticles with various sizes, porosities, and shapes by drying colloidal dispersion drops on liquid repellent surfaces. Until now, for the method, only spherical shaped colloidal particles have been used as primary colloids. Here, we introduce six different shapes of nano-colloidal dispersions for the STED method: nanocubics, nanoplates, nanosheets, coffin-shaped nanoparticles (NPs), spherical NPs, and aggregates of NPs. It is confirmed that the shape and size of the primary colloids have little effect for drying the dispersion drop when a single component colloidal dispersion is dried. For heterogeneous supraparticles with composite material assembly, still the shape of the colloids has no influences, while the size and dispersity play roles for tuning the morphology of the supraparticles. From the results, we propose a way to fabricate homogeneous mixture, core/shell, and Janus core/shell structures of the supraparticles depending on the size and dispersity of the mixture colloidal dispersion. Indeed, knowledge on the effects of types of colloids would be of great importance for tailoring supraparticles

Tailoring the Morphology of Supraparticles by Primary Colloids with Different Shapes, Sizes and Dispersities

Surface-templated evaporation driven (STED) method is a promising method to fabricate supraparticles with various sizes, porosities, and shapes by drying colloidal dispersion drops on liquid repellent surfaces. Until now, for the method, only spherical shaped colloidal particles have been used as primary colloids. Here, we introduce six different shapes of nano-colloidal dispersions for the STED method: nanocubics, nanoplates, nanosheets, coffin-shaped nanoparticles (NPs), spherical NPs, and aggregates of NPs. It is confirmed that the shape and size of the primary colloids have little effect for drying the dispersion drop when a single component colloidal dispersion is dried. For heterogeneous supraparticles with composite material assembly, still the shape of the colloids has no influences, while the size and dispersity play roles for tuning the morphology of the supraparticles. From the results, we propose a way to fabricate homogeneous mixture, core/shell, and Janus core/shell structures of the supraparticles depending on the size and dispersity of the mixture colloidal dispersion. Indeed, knowledge on the effects of types of colloids would be of great importance for tailoring supraparticles

The Effect of Varying Slice Thickness and Interslice Gap on T-1 and T-2 Measured with the Multidynamic Multiecho Sequence

Purpose: The purpose of our study was to investigate the effect of different slice thicknesses and/or interslice gaps on longitudinal and transverse relaxation times (T-1 and T-2) measured by a multi-dynamic, multi-echo (MDME) sequence. Materials and Methods: This retrospective study included nine healthy subjects who underwent MDME sequence (at 3T) with four different combinations of slice thicknesses and/or interslice gaps: slice thickness of 4 mm and interslice gap of 0 mm (TH4/G0), TH4/G1, TH5/G0, and TH5/G1. T-1 and T-2 were measured in various brain regions by a qualified neuroradiologist with 8 years of clinical experience: the frontal white matter (WM), occipital WM, genu, splenium, frontal cortex, thalamus, putamen, caudate head, and cerebrospinal fluid (CSF). The paired samples t-test was used to investigate the effect of different slice thicknesses and interslice gaps (TH4/G0 versus TH4/G1 and TH5/G0 versus TH5/G1). P 0.013). In addition, T-1 in all brain regions of interest did not significantly change between TH4/G0, TH4/G1, TH5/G0 and TH5/G1. However, T-1 in some of the brain regions was higher with TH4/G0 than with TH5/G0 (occipital WM, frontal cortex, and caudate head) and with TH4/G1 than with TH5/G1 (occipital WM, genu, splenium and thalamus, all Ps < 0.013). Conclusion: T-2 estimated using the MDME sequence was stable regardless of slice thickness or gap. Although the sequence seems to provide stable relaxation values, identical slice thicknesses need to be used for follow-up to prevent potential T-1 changes. ©2018 Japanese Society for Magnetic Resonance in Medicine11sci

Multiple Facets of Nitrogen: From Atmospheric Gas to Indispensable Agricultural Input

Nitrogen (N) is a gas and the fifth most abundant element naturally found in the atmosphere. N&rsquo;s role in agriculture and plant metabolism has been widely investigated for decades, and extensive information regarding this subject is available. However, the advent of sequencing technology and the advances in plant biotechnology, coupled with the growing interest in functional genomics-related studies and the various environmental challenges, have paved novel paths to rediscovering the fundamentals of N and its dynamics in physiological and biological processes, as well as biochemical reactions under both normal and stress conditions. This work provides a comprehensive review on multiple facets of N and N-containing compounds in plants disseminated in the literature to better appreciate N in its multiple dimensions. Here, some of the ancient but fundamental aspects of N are revived and the advances in our understanding of N in the metabolism of plants is portrayed. It is established that N is indispensable for achieving high plant productivity and fitness. However, the use of N-rich fertilizers in relatively higher amounts negatively affects the environment. Therefore, a paradigm shift is important to shape to the future use of N-rich fertilizers in crop production and their contribution to the current global greenhouse gases (GHGs) budget would help tackle current global environmental challenges toward a sustainable agriculture