Local Positional Encoding for Multi-Layer Perceptrons

A multi-layer perceptron (MLP) is a type of neural networks which has a long history of research and has been studied actively recently in computer vision and graphics fields. One of the well-known problems of an MLP is the capability of expressing high-frequency signals from low-dimensional inputs. There are several studies for input encodings to improve the reconstruction quality of an MLP by applying pre-processing against the input data. This paper proposes a novel input encoding method, local positional encoding, which is an extension of positional and grid encodings. Our proposed method combines these two encoding techniques so that a small MLP learns high-frequency signals by using positional encoding with fewer frequencies under the lower resolution of the grid to consider the local position and scale in each grid cell. We demonstrate the effectiveness of our proposed method by applying it to common 2D and 3D regression tasks where it shows higher-quality results compared to positional and grid encodings, and comparable results to hierarchical variants of grid encoding such as multi-resolution grid encoding with equivalent memory footprint

Specific Rab GTPase-activating proteins define the Shiga toxin and epidermal growth factor uptake pathways

Rab family guanosine triphosphatases (GTPases) together with their regulators define specific pathways of membrane traffic within eukaryotic cells. In this study, we have investigated which Rab GTPase-activating proteins (GAPs) can interfere with the trafficking of Shiga toxin from the cell surface to the Golgi apparatus and studied transport of the epidermal growth factor (EGF) from the cell surface to endosomes. This screen identifies 6 (EVI5, RN-tre/USP6NL, TBC1D10A–C, and TBC1D17) of 39 predicted human Rab GAPs as specific regulators of Shiga toxin but not EGF uptake. We show that Rab43 is the target of RN-tre and is required for Shiga toxin uptake. In contrast, RabGAP-5, a Rab5 GAP, was unique among the GAPs tested and reduced the uptake of EGF but not Shiga toxin. These results suggest that Shiga toxin trafficking to the Golgi is a multistep process controlled by several Rab GAPs and their target Rabs and that this process is discrete from ligand-induced EGF receptor trafficking

Inhibitory Effect of Flavonoids on the Efflux of N-Acetyl 5-Aminosalicylic Acid Intracellularly Formed in Caco-2 Cells

N-acetyl 5-aminosalicylic acid (5-AcASA) that was intracellularly formed from 5-aminosalicylic acid (5-ASA) at 200 μM was discharged 5.3, 7.1, and 8.1-fold higher into the apical site than into the basolateral site during 1, 2, and 4-hour incubations, respectively, in Caco-2 cells grown in Transwells. The addition of flavonols (100 μM) such as fisetin and quercetin with 5-ASA remarkably decreased the apically directed efflux of 5-AcASA. When 5-ASA (200 μM) was added to Caco-2 cells grown in tissue culture dishes, the formation of 5-AcASA decreased, and, in addition, the formed 5-AcASA was found to be accumulated within the cells in the presence of such flavonols. Thus, the decrease in 5-AcASA efflux by such flavonols was attributed not only to the inhibition of N-acetyl-conjugation of 5-ASA but to the predominant cellular accumulation of 5-AcASA. Various flavonoids also had both of the effects with potencies that depend on their specific structures. The essential structure of flavonoids was an absence of a hydroxyl substitution at the C5 position on the A-ring of flavone structure for the inhibitory effect on the N-acetyl-conjugation of 5-ASA, and a presence of hydroxyl substitutions at the C3′ or C4′ position on the B-ring of flavone structure for the promoting effect on the cellular accumulation of 5-AcASA. Both the decrease in 5-AcASA apical efflux and the increase in 5-AcASA cellular accumulation were also caused by MK571 and indomethacin, inhibitors of MRPs, but not by quinidine, cyclosporin A, P-glycoprotein inhibitors, and mitoxantrone, a BCRP substrate. These results suggest that certain flavonoids suppress the apical efflux of 5-AcASA possibly by inhibiting MRPs pumps located on apical membranes in Caco-2 cells

Evolutionary loss of thermal acclimation accompanied by periodic monocarpic mass flowering in Strobilanthes flexicaulis

While life history, physiology and molecular phylogeny in plants have been widely studied, understanding how physiology changes with the evolution of life history change remains largely unknown. In two closely related understory Strobilanthes plants, the molecular phylogeny has previously shown that the monocarpic 6-year masting S. flexicaulis have evolved from a polycarpic perennial, represented by the basal clade S. tashiroi. The polycarpic S. tashiroi exhibited seasonal thermal acclimation with increased leaf respiratory and photosynthetic metabolism in winter, whereas the monocarpic S. flexicaulis showed no thermal acclimation. The monocarpic S. flexicaulis required rapid height growth after germination under high intraspecific competition, and the respiration and N allocation were biased toward nonphotosynthetic tissues. By contrast, in the long-lived polycarpic S. tashiroi, these allocations were biased toward photosynthetic tissues. The life-history differences between the monocarpic S. flexicaulis and the polycarpic S. tashiroi are represented by the “height growth” and “assimilation” paradigms, respectively, which are controlled by different patterns of respiration and nitrogen regulation in leaves. The obtained data indicate that the monocarpic S. flexicaulis with the evolutionary loss of thermal acclimation may exhibit increased vulnerability to global warming

White dots as a novel marker of diabetic retinopathy severity in ultrawide field imaging

Purpose: To characterize white dots in diabetic retinopathy (DR) and their association with disease severity using ultra-wide-field scanning laser ophthalmoscopy. Methods: We randomly selected 125 eyes of 77 patients (25 eyes from individual categories of the international classification of DR severity) for which ultrawide field photographs were obtained. We characterized white dots, which were delineated by higher signal levels on green but not red laser images, and evaluated the relationship between the number of white dots and the international severity scale of DR. Results: Most white dots were located in nonperfused areas, and the number of total white dots was significantly correlated to that of dots in nonperfused areas. White dots corresponded to microaneurysms around the boundary between nonperfused areas and perfused areas or unknown lesions in nonperfused areas. Eyes with DR had significantly more white dots than those with no apparent retinopathy. The numbers of white dots in moderate nonproliferative diabetic retinopathy (NPDR) or more severe grades were significantly higher than in mild NPDR. The area under the receiver operating characteristics curve (AROC) analyses demonstrated that the number of white dots had the significance in the diagnosis of DR (0.908-0.986) and moderate NPDR or more severe grades (0.888-0.974). Conclusions: These data suggest the clinical relevance of white dots seen on ultrawide field images in the diagnosis of the severity of DR

Tree hazards compounded by successive climate extremes after masting in a small endemic tree, Distylium lepidotum , on subtropical islands in Japan

連続して生じる異常気象は樹木の衰退を加速させる --地球温暖化の森林への影響を高精度に予測する道を開く成果--. 京都大学プレスリリース. 2021-09-28.Ongoing global warming increases the frequency and severity of tropical typhoons and prolonged drought, leading to forest degradation. Simultaneous and/or successive masting events and climatic extremes may thus occur frequently in the near future. If these climatic extremes occur immediately after mass seed reproduction, their effects on individual trees are expected to be very severe because mass reproduction decreases carbohydrate reserves. While the effects of either a single climate extreme or masting alone on tree resilience/growth have received past research attention, understanding the cumulative effects of such multiple events remains challenging and is crucial for predicting future forest changes. Here, we report tree hazards compound by two successive climate extremes, a tropical typhoon and prolonged drought, after mass reproduction in an endemic tree species (Distylium lepidotum Nakai) on oceanic islands. Across individual trees, the starch stored within the sapwood of branchlets significantly decreased with reproductive efforts (fruit mass/shoot mass ratio). Typhoon damage significantly decreased not only the total leaf area of apical shoots but also the maximum photosynthetic rates. During the 5-month period after the typhoon, the mortality of large branchlets (8–10-mm diameter) increased with decreasing stored starch when the typhoon hit. During the prolonged summer drought in the next year, the recovery of total leaf area, stored starch, and hydraulic conductivity was negatively correlated with the stored starch at the typhoon. These data indicate that the level of stored starch within branchlets is the driving factor determining tree regrowth or dieback, and the restoration of carbohydrates after mass reproduction is synergistically delayed by such climate extremes. Stored carbohydrates are the major cumulative factor affecting individual tree resilience, resulting in their historical effects. Because of highly variable carbohydrate levels among individual trees, the resultant impacts of such successive events on forest dieback will be fundamentally different among trees

Functional dissection of Rab GTPases involved in primary cilium formation

Primary cilia are sensory structures involved in morphogen signalling during development, liquid flow in the kidney, mechanosensation, sight, and smell (Badano, J.L., N. Mitsuma, P.L. Beales, and N. Katsanis. 2006. Annu. Rev. Genomics Hum. Genet. 7:125–148; Singla, V., and J.F. Reiter. 2006. Science. 313:629–633.). Mutations that affect primary cilia are responsible for several diseases, including neural tube defects, polycystic kidney disease, retinal degeneration, and cancers (Badano et al., 2006; Singla and Reiter, 2006). Primary cilia formation and function requires tight integration of the microtubule cytoskeleton with membrane trafficking (Singla and Reiter, 2006), and this is poorly understood. We show that the Rab GTPase membrane trafficking regulators Rab8a, -17, and -23, and their cognate GTPase-activating proteins (GAPs), XM_037557, TBC1D7, and EVI5like, are involved in primary cilia formation. However, other human Rabs and GAPs are not. Additionally, Rab8a specifically interacts with cenexin/ODF2, a basal body and microtubule binding protein required for cilium biogenesis (Ishikawa, H., A. Kubo, S. Tsukita, and S. Tsukita. 2005. Nat. Cell Biol. 7:517–524), and is the sole Rab enriched at primary cilia. These findings provide a basis for understanding how specific membrane trafficking pathways cooperate with the microtubule cytoskeleton to give rise to the primary cilia

Psychosocial functioning in patients with treatment-resistant depression after group cognitive behavioral therapy

<p>Abstract</p> <p>Background</p> <p>Although patients with Treatment Resistant Depression (TRD) often have impaired social functioning, few studies have investigated the effectiveness of psychosocial treatment for these patients. We examined whether adding group cognitive behavioral therapy (group-CBT) to medication would improve both the depressive symptoms and the social functioning of patient with mild TRD, and whether any improvements would be maintained over one year.</p> <p>Methods</p> <p>Forty-three patients with TRD were treated with 12 weekly sessions of group-CBT. Patients were assessed with the Global Assessment of Functioning scale (GAF), the 36-item Short-Form Health Survey (SF-36), the Hamilton Rating Scale for Depression (HRSD), the Dysfunctional Attitudes Scale (DAS), and the Automatic Thought Questionnaire-Revised (ATQ-R) at baseline, at the termination of treatment, and at the 12-month follow-up.</p> <p>Results</p> <p>Thirty-eight patients completed treatment; five dropped out. For the patients who completed treatment, post-treatment scores on the GAF and SF-36 were significantly higher than baseline scores. Scores on the HRSD, DAS, and ATQ-R were significantly lower after the treatment. Thus patients improved on all measurements of psychosocial functioning and mood symptoms. Twenty patients participated in the 12-month follow-up. Their improvements for psychosocial functioning, depressive symptoms, and dysfunctional cognitions were sustained at 12 months following the completion of group-CBT.</p> <p>Conclusions</p> <p>These findings suggest a positive effect that the addition of cognitive behavioural group therapy to medication on depressive symptoms and social functioning of mildly depressed patients, showing treatment resistance.</p

Physiological mechanisms of drought-induced tree die-off in relation to carbon, hydraulic and respiratory stress in a drought-tolerant woody plant

Drought-induced tree die-off related to climate change is occurring worldwide and affects the carbon stocks and biodiversity in forest ecosystems. Hydraulic failure and carbon starvation are two commonly proposed mechanisms for drought-induced tree die-off. Here, we show that inhibited branchlet respiration and soil-to-leaf hydraulic conductance, likely caused by cell damage, occur prior to hydraulic failure (xylem embolism) and carbon starvation (exhaustion of stored carbon in sapwood) in a drought-tolerant woody species, Rhaphiolepis wrightiana Maxim. The ratio of the total leaf area to the twig sap area was used as a health indicator after drought damage. Six adult trees with different levels of tree health and one dead adult tree were selected. Two individuals having the worst and second worst health among the six live trees died three months after our study was conducted. Soil-to-leaf hydraulic conductance and leaf gas exchange rates decreased linearly as tree health declined, whereas xylem cavitation and total non-structural carbon remained unchanged in the branchlets except in the dead and most unhealthy trees. Respiration rates and the number of living cells in the sapwood decreased linearly as tree health declined. This study is the first report on the importance of dehydration tolerance and respiration maintenance in living cells

Gene Expression Profiles of the Cochlea and Vestibular Endorgans: Localization and Function of Genes Causing Deafness

Objectives: We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss. Methods: Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Honnepage using localization, expression, and distribution as keywords. Results: Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans. Conclusions: The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.ArticleANNALS OF OTOLOGY RHINOLOGY AND LARYNGOLOGY. 124:6S-48S (2015)journal articl