Miracle-dz/UniFAR-FTUs huggingface dataset:
A Precision B Cell–Targeted Therapeutic Approach to Autoimmunity Caused by Phosphatidylinositol 3-Kinase Pathway Dysregulation

Key Points Low-dosage p110δ inhibitor therapy prevents PTEN- but not SHP-1–driven autoimmunity. Effective p110δ inhibitor dosages spare immune responses to exogenous immunogens. Low-dosage p110δ inhibitor therapy delays T1D progression in VH125.NOD mice. Visual Abstract The inositol lipid phosphatases PTEN and SHIP-1 play a crucial role in maintaining B cell anergy and are reduced in expression in B cells from systemic lupus erythematosus and type 1 diabetes patients, consequent to aberrant regulation by miRNA-7 and 155. With an eye toward eventual use in precision medicine therapeutic approaches in autoimmunity, we explored the ability of p110δ inhibition to compensate for PI3K pathway dysregulation in mouse models of autoimmunity. Low dosages of the p110δ inhibitor idelalisib, which spare the ability to mount an immune response to exogenous immunogens, are able to block the development of autoimmunity driven by compromised PI3K pathway regulation resultant from acutely induced B cell–targeted haploinsufficiency of PTEN and SHIP-1. These conditions do not block autoimmunity driven by B cell loss of the regulatory tyrosine phosphatase SHP-1. Finally, we show that B cells in NOD mice express reduced PTEN, and low-dosage p110δ inhibitor therapy blocks disease progression in this model of type 1 diabetes. These studies may aid in the development of precision treatments that act by enforcing PI3K pathway regulation in patients carrying specific risk alleles.
Tracking multiple moving object based on combined color and centroid feature in video sequence

Object motion tracking has been done for videos with various methodologies. The existing systems are mainly based on single feature and motion detection as a single object by taking the movement of the feature selected. We propose a moving object tracking method that uses low-level features like centroid location of tracked object combined with the color feature. Centroid location of each moving object in the current frame is computed using the greedy technique based on previous locations of the object in earlier frame. Experimental result shows that the proposed tracking approach detects and tracks object moving in the scene efficiently and also can handle occlusion.
CRYSPLOT: A new tool to visualize physical and chemical properties of molecules, polymers, surfaces, and crystalline solids

CRYSPLOT is a web‐oriented tool (http://crysplot.crystalsolutions.eu) to visualize computed properties of periodic systems, in particular, as computed with the CRYSTAL code. Along with plotting, CRYSPLOT also permits the modification and customization of plots to meet the standards required for scientific graphics. CRYSPLOT has been designed with advanced and freely available graphical Javascript libraries as Plotly. The programming language used is Javascript. The code parses the input files, reads the data, and organizes them into objects ready to be plotted with the plotly.js library. It is modular and flexible so that it is very simple to add other input data formats. The new graphical tool is presented in details along with selected applications on metal–organic frameworks to show some of its capabilities. © 2019 Wiley Periodicals, Inc.
Classification and visualization of the social science network by the minimum span clustering method

We propose a minimum span clustering (MSC) method for clustering and visualizing complex networks using the interrelationship of network components. To demonstrate this method, it is applied to classify the social science network in terms of aggregated journal-journal citation relations of the Institute of Scientific Information (ISI) Journal Citation Reports. This method of network classification is shown to be efficient, with a processing time that is linear to network size. The classification results provide an in-depth view of the network structure at various scales of resolution. For the social science network, there are 4 resolution scales, including 294 batches of journals at the highest scale, 65 categories of journals at the second, 15 research groups at the third scale, and 3 knowledge domains at the lowest resolution. By comparing the relatedness of journals within clusters, we show that our clustering method gives a better classification of social science journals than ISI's heuristic approach and hierarchical clustering. In combination with the minimum spanning tree approach and multi-dimensional scaling, MSC is also used to investigate the general structure of the network and construct a map of the social science network for visualization. © 2011 Wiley Periodicals, Inc.
Screening and Characterization of Drugs That Protect Corneal Endothelial Cells Against Unfolded Protein Response and Oxidative Stress

Purpose To screen for and characterize compounds that protect corneal endothelial cells against unfolded protein response (UPR) and oxidative stress. Methods Bovine corneal endothelial cells (BCECs) were treated for 48 hours with 640 compounds from a Food and Drug Administration (FDA)-approved drug library and then challenged with thapsigargin or H2O2 to induce UPR or oxidative stress, respectively. Cell viability was measured using the CellTiter-Glo survival assay. Selected “hits” were subjected to further dose-response testing, and their ability to modulate expression of UPR and oxidative stress markers was assessed by RT-PCR, Western blot, and measurement of protein carbonyl and 8-hydroxydeoxyguanosine (8-OHdG) adducts in immortalized human corneal endothelial cells (iHCECs). Results Forty-one drugs at 20 μM and 55 drugs at 100 μM increased survival of H2O2-challenged cells, and 8 drugs at 20 μM and 2 drugs at 100 μM increased survival of thapsigargin-challenged cells, compared with untreated control cells. Nicergoline, ergothioneine, nimesulide, oxotremorine, and mefenamic acid increased survival of both H2O2- and thapsigargin-challenged cells. Oxotremorine altered DNA damage inducible 3 (CHOP) gene expression, glucose-regulated protein 78 kDa (GRP78) and activating transcription factor 4 (ATF4) protein expression, and protein carbonyl and 8-OHdG levels. Mefenamic acid altered GRP78 protein expression and protein carbonyl and 8-OHdG levels. Conclusions Oxotremorine and mefenamic acid are potential survival factors for corneal endothelial cells under UPR and oxidative stress. The described assay can be further expanded to screen additional drugs for potential therapeutic effect in corneal endothelial diseases such as Fuchs' endothelial corneal dystrophy.
Metformin induces a fasting- and antifolate-mimicking modification of systemic host metabolism in breast cancer patients

Certain dietary interventions might improve the therapeutic index of cancer treatments. An alternative to the “drug plus diet” approach is the pharmacological reproduction of the metabolic traits of such diets. Here we explored the impact of adding metformin to an established therapeutic regimen on the systemic host metabolism of cancer patients. A panel of 11 serum metabolites including markers of mitochondrial function and intermediates/products of folate-dependent one-carbon metabolism were measured in paired baseline and post-treatment sera obtained from HER2-positive breast cancer patients randomized to receive either metformin combined with neoadjuvant chemotherapy and trastuzumab or an equivalent regimen without metformin. Metabolite profiles revealed a significant increase of the ketone body β-hydroxybutyrate and of the TCA intermediate α-ketoglutarate in the metformin-containing arm. A significant relationship was found between the follow-up levels of homocysteine and the ability of treatment arms to achieve a pathological complete response (pCR). In the metformin-containing arm, patients with significant elevations of homocysteine tended to have a higher probability of pCR. The addition of metformin to an established anti-cancer therapeutic regimen causes a fasting-mimicking modification of systemic host metabolism. Circulating homocysteine could be explored as a clinical pharmacodynamic biomarker linking the antifolate-like activity of metformin and biological tumor response.
LifeLogOn: A Practical Lifelog System for Building and Exploiting Lifelog Ontology

In this paper, we aim to overcome barriers to realizing practical lifelog systems, and we propose a lifelog system named ‘LifeLogOn’ (Lifelog Ontology; ‘Log on to your lifelogs’). The system allows users to easily build and exploit lifelog ontology by importing various available data sources. In addition, we present some use case scenarios to show how our system and the lifelog ontology built by our system can be used for many purposes.
Joint Optimization of Interference Coordination Parameters and Base-Station Density for Energy-Efficient Heterogeneous Networks

Heterogeneous networks (HetNets), consisting of macro-cells and overlaying pico-cells, have been recognized as a promising paradigm to support the exponential growth of data traffic demands and high network energy efficiency (EE). However, for two-tier heterogeneous architecture deployment of HetNets, the inter-tier interference will be challenging. Time domain further-enhanced inter-cell interference coordination (FeICIC) proposed in 3GPP Release-11 becomes necessary to mitigate the inter-tier interference by applying low power almost blank subframe (ABS) scheme. Therefore, for HetNets deployment in reality, the pico-cell range expansion (CRE) bias, the power of ABS and the density of pico base stations (PBSs) are three important factors for the network EE improvement. Aiming to improve the network EE, the above three factors are jointly considered in this paper. In particular, we first derive the closed-form expression of the network EE as a function of pico CRE bias, power reduction factor of low power ABS and PBS density based on stochastic geometry model. Then, the approximate relationship between pico CRE bias and power reduction factor is deduced, followed by a linear search algorithm to get the near-optimal pico CRE bias and power reduction factor together at a given PBS density. Next, a linear search algorithm is further proposed to optimize PBS density based on fixed pico CRE bias and power reduction factor. Due to the fact that the above pico CRE bias and power reduction factor optimization and PBS density optimization are optimized separately, a heuristic algorithm is further proposed to optimize pico CRE bias, power reduction factor and PBS density jointly to achieve global network EE maximization. Numerical simulation results show that our proposed heuristic algorithm can significantly enhance the network EE while incurring low computational complexity.
Lin28a Protects against Hypoxia/Reoxygenation Induced Cardiomyocytes Apoptosis by Alleviating Mitochondrial Dysfunction under High Glucose/High Fat Conditions

Aim The aim of the present study was to investigate the role of Lin28a in protecting against hypoxia/reoxygenation (H/R)-induced cardiomyocytes apoptosis under high glucose/high fat (HG/HF) conditions. Methods Primary cardiomyocytes which were isolated from neonatal mouse were randomized to be treated with lentivirus carrying Lin28a siRNA, Lin28acDNA 72 h before H/R (9 h/2 h). Cardiomyocytes biomarkers release (LDH and CK), cardiomyocytes apoptosis, mitochondria biogenesis and morphology, intracellular reactive oxygen species (ROS) production, ATP content and inflammatory cytokines levels after H/R injury in high glucose/high fat conditions were compared between groups. The target proteins of Lin28a were examined by western blot analysis. Results Our results revealed that Lin28a cDNA transfection (overexpression) significantly inhibited cardiomyocyte apoptotic index, improved mitochondria biogenesis, increased ATP production and reduced ROS production as compared with the H/R group in HG/HF conditions. Lin28a siRNA transfection (knockdown) rendered the cardiomyocytes more susceptible to H/R injury as evidenced by increased apoptotic index, impaired mitochondrial biogenesis, decreased ATP production and increased ROS level. Interestingly, these effects of Lin28a were blocked by pretreatment with the PI3K inhibitor wortmannin. Lin28a overexpression increased, while Lin28a knockdown inhibited IGF1R, Nrf-1, Tfam, p-IRS-1, p-Akt, p-mTOR, p-p70s6k, p-AMPK expression levels after H/R injury in HG/HF conditions. Moreover, pretreatment with wortmannin abolished the effects of Lin28a on the expression levels of p-AKT, p-mTOR, p-p70s6k, p-AMPK. Conclusions The present results suggest that Lin28a inhibits cardiomyocytes apoptosis by enhancing mitochondrial biogenesis and function under high glucose/high fat conditions. The mechanism responsible for the effects of Lin28a is associated with the PI3K/Akt dependent pathway.
Visual Topography of Human Intraparietal Sulcus

Human parietal cortex is implicated in a wide variety of sensory and cognitive functions, yet its precise organization remains unclear. Visual field maps provide a potential structural basis for descriptions of functional organization. Here, we detail the topography of a series of five maps of the contralateral visual hemifield within human posterior parietal cortex. These maps are located along the medial bank of the intraparietal sulcus (IPS) and are revealed by direct visual stimulation during functional magnetic resonance imaging, allowing these parietal regions to be routinely and reliably identified simultaneously with occipital visual areas. Two of these maps (IPS3 and IPS4) are novel, whereas two others (IPS1 and IPS2) have previously been revealed only by higher-order cognitive tasks. Area V7, a previously identified visual map, is observed to lie within posterior IPS and to share a foveal representation with IPS1. These parietal maps are reliably observed across scan sessions; however, their precise topography varies between individuals. The multimodal organization of posterior IPS mirrors this variability in visual topography, with complementary tactile activations found immediately adjacent to the visual maps both medially and laterally. These visual maps may provide a practical framework in which to characterize the functional organization of human IPS.
Explanation closure as a knowledge representation tool for automated story generation

Computer scientists employ knowledge representation schemes to represent the semantic content of natural language concepts. Representation of knowledge means using a formal language to compose descriptions that correspond to the world. The interest in artificial intelligence is developing descriptions of the world in such a way that an intelligent machine can come to new conclusions about its environment by using these descriptions. This paper describes the construction of a formal world model for the Joseph system, a set of programs in the Prolog language which generates short narratives modeled after Russian folktales. The Joseph system uses interchangeable world models as its source for the facts and events around which the stories revolve. A world model in the Joseph system is a set of prolog predicates which describe the potential characters, events, and range of reactions to events that drive the plot of the story. In the paper, I describe the world model predicates, discuss shortcomings in the present implementation of the system, and present possible solutions to these shortcomings.
Cryostructuring of Polymeric Systems. 52. Properties, Microstructure and an Example of a Potential Biomedical Use of the Wide-Pore Alginate Cryostructurates

Wide-pore cryostructurates were prepared via freezing sodium alginate aqueous solutions with subsequent ice sublimation from the frozen samples, followed by their incubation in the ethanol solutions of calcium chloride or sulfuric acid, rinsing, and final drying. Such sequence of operations resulted in the calcium alginate or alginic acid sponges, respectively. The swelling degree of the walls of macropores in such matrices decreased with increasing polymer concentration in the initial solution. The dependence of the degree of swelling on the cryogenic processing temperature had a bell-like character with a maximum for the samples formed at −20 °C. According to 1H NMR spectroscopy, the content of mobile (non-frozen) water in the frozen water-sodium alginate systems also depended on the initial polymer concentration and freezing temperature. The cryostructurates obtained did not lose their integrity in water, saline, in an acidic medium at pH 2 for at least three weeks. Under alkaline conditions at pH 12 the first signs of dissolution of the Ca-alginate sponge arose only after a week of incubation. Microbiological testing of the model depot form of the antibiotics entrapped in the Ca-alginate cryostructurate demonstrated the efficiency of this system as the antibacterial material.
Serum Ethylamine Levels as an Indicator of l-Theanine Consumption and the Risk of Type 2 Diabetes in a General Japanese Population: The Hisayama Study

OBJECTIVE This study investigated the association between serum ethylamine levels as an indicator of l-theanine consumption and the development of type 2 diabetes in a Japanese community. RESEARCH DESIGN AND METHODS A total of 2,253 community-dwelling Japanese individuals aged 40–79 years without diabetes were monitored for 7 years. Serum ethylamine levels were divided into quartiles: ≤0.86, 0.87–2.10, 2.11–5.28, and ≥5.29 ng/mL. Kinetic analysis of serum ethylamine concentrations was performed after ingestion of l-theanine–rich green tea products containing 8 mg of l-theanine by 12 healthy volunteers. RESULTS During follow-up, 282 subjects developed type 2 diabetes. The age- and sex-adjusted cumulative incidence of type 2 diabetes decreased significantly with elevating levels of serum ethylamine (P for trend = 0.04). This association remained unchanged after adjusting for potential confounding factors. The multivariable-adjusted hazard ratio (HR) for type 2 diabetes was significantly lower in the fourth quartile of serum ethylamine than in the first quartile (HR 0.69, 95% CI 0.49–0.98). This trend of decrease in diabetic risk across serum ethylamine levels was more prominent in middle-aged subjects and in subjects with prediabetes, obesity, or insulin resistance. Kinetic analysis estimated that the minimum concentration at the steady state was >5.90 ng/mL in the case of twice-daily ingestion with an interval of 12 h. CONCLUSIONS Higher serum ethylamine was significantly associated with lower risk of the development of type 2 diabetes in a general Japanese population. The measurement of serum ethylamine concentration would be a useful biomarker for the objective estimation of l-theanine consumption.
A Robust Noise Mitigation Method for the Mobile RFID Location in Built Environment

The exact location of objects, such as infrastructure, is crucial to the systematic understanding of the built environment. The emergence and development of the Internet of Things (IoT) have attracted growing attention to the low-cost location scheme, which can respond to a dramatic increasing amount of public infrastructure in smart cities. Various Radio Frequency IDentification (RFID)-based locating systems and noise mitigation methods have been developed. However, most of them are impractical for built environments in large areas due to their high cost, computational complexity, and low noise detection capability. In this paper, we proposed a novel noise mitigation solution integrating the low-cost localization scheme with one mobile RFID reader. We designed a filter algorithm to remove the influence of abnormal data. Inspired the sampling concept, a more carefully parameters calibration was carried out for noise data sampling to improve the accuracy and reduce the computational complexity. To achieve robust noise detection results, we employed the powerful noise detection capability of the random sample consensus (RANSAC) algorithm. Our experiments demonstrate the effectiveness and advantages of the proposed method for the localization and noise mitigation in a large area. The proposed scheme has potential applications for location-based services in smart cities.
CoffeebEST: an integrated resource for Coffea spp expressed sequence tags.

Coffee is one of the most important commodities in the world, and its production relies mainly on two species, Coffea arabica and Coffea canephora. Although there are diverse transcriptome datasets available for coffee trees, few research groups have exploited the potential knowledge contained in these data, especially with respect to fruit and seed development. Here, we present a comparative analysis of the transcriptomes of Coffea arabica and Coffea canephora with a focus on fruit development using publicly available expressed sequence tags (ESTs). Most of the fruit and seed EST data has been obtained from C. canephora. Therefore, we performed a fruit EST analysis of the 5 developmental stages of this species (18, 22, 30, 42, and 46 weeks after flowering) comprising 29,009 sequences. We compared C. canephora fruit ESTs to reference unigenes of C. canephora (7710 contigs and 8955 singletons) and C. arabica (15,656 contigs and 16,351 singletons). Additional analyses included functional annotation based on Gene Onthology, as well as an annotation using PlantCyc, a curated plant protein database. The Coffee Bean EST (CoffeebEST) is a public database available at http://bioinfo-02.cp. utfpr.edu. br/. This database represents an additional resource for the coffee scientific community, offering a user-friendly collection of information for non-specialists in coffee molecular biology to support experimental research on comparative and functional genomics.
High-resolution hyperspectral imaging via matrix factorization

Hyperspectral imaging is a promising tool for applications in geosensing, cultural heritage and beyond. However, compared to current RGB cameras, existing hyperspectral cameras are severely limited in spatial resolution. In this paper, we introduce a simple new technique for reconstructing a very high-resolution hyperspectral image from two readily obtained measurements: A lower-resolution hyper-spectral image and a high-resolution RGB image. Our approach is divided into two stages: We first apply an unmixing algorithm to the hyperspectral input, to estimate a basis representing reflectance spectra. We then use this representation in conjunction with the RGB input to produce the desired result. Our approach to unmixing is motivated by the spatial sparsity of the hyperspectral input, and casts the unmixing problem as the search for a factorization of the input into a basis and a set of maximally sparse coefficients. Experiments show that this simple approach performs reasonably well on both simulations and real data examples.
Advances Toward Image Understanding of Multimodal Volume Data

This paper introduces new work in multiscale image statistics, a local framework that supports adaptive measurement of image structure where data may be represented by multiple incommensurable values. Data such as those represented by the Visible Human Project data often include multiple modalities such as color channels, multiple pulse sequences of magnetic resonance imaging, and X-ray CT data. Multiscale statistics can establish local correlations, covariances, and entropy measurements across the image. Such measurements have applications in nonlinear filtering, texture analysis, deformable registration and image segmentation.