gebhart/patrepeval huggingface dataset:
Lipopolysaccharide-induced reductions in body weight gain and feed intake do not reduce the efficiency of arginine utilization for whole-body protein accretion in the chick (1998)

The effects of repeated injections of 400 microg Escherichia coli lipopolysaccharide (LPS) on chick performance from 11 to 22 d posthatching were examined in chicks fed casein-based diets containing graded levels of arginine. Administration of LPS reduced (P < 0.05) weight gain, feed intake, and protein accretion, and there was a tendency (P=0.07) for LPS administration to be more growth-depressing at the higher than at the lower levels of supplemental arginine. Regression analysis of protein accretion for the first three doses of arginine indicated that protein accretion was a linear (P < 0.01) function of supplemental arginine intake for both saline-injected (r2=0.94) and LPS-injected (r2=0.93) chicks. Slopes of the best-fit regression lines for both treatment groups were equal, indicating that arginine utilization for protein accretion was not affected by LPS administration. The dietary arginine concentration required to maximize weight gain and feed efficiency was unaffected by LPS administration, with both saline- and LPS-injected chicks reaching plateaus in weight gain and feed efficiency at 0.90 and 0.98% digestible arginine, respectively.
Dynamic Encoder/Decoder Based on Fiber Bragg Gratings for Optical Security System (2004)

A novel dynamic encoder/decoder based on fiber Bragg gratings for optical security systems is presented in this paper. The encoded and decoded optical communication signals can be realized by controlling the optical switches and fiber Bragg grating arrangement. We describe the system operation principle and set up an experimental encoder/decoder to demonstrate the feasibility of the proposed scheme.
The systematic design and biophysical evaluation of cationic sulfonamide aminolipids for siRNA delivery (2016)

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Fast string searching in secondary storage: theoretical developments and experimental results (1996)

In a previous work, we proposed a text indexing data structure for secondary storage, which we called SB-tree, that combines the best of B-trees and suffix arrays, overcoming the limitations of inverted files, suffix arrays, suffix trees, and prefix B-trees. In this paper we study the performance of SB-trees in a practical setting, performing a set of searching and updating experiments. Improved performance was obtained by a new space efficient and alphabet-independent organization of the internal nodes of the SB-tree, and a new batch insertion procedure that avoids thrashing.
Automatic localization of bifurcations and vessel crossings in digital fundus photographs using location regression (2011)

Parameters extracted from the vasculature on the retina are correlated with various conditions such as diabetic retinopathy and cardiovascular diseases such as stroke. Segmentation of the vasculature on the retina has been a topic that has received much attention in the literature over the past decade. Analysis of the segmentation result, however, has only received limited attention with most works describing methods to accurately measure the width of the vessels. Analyzing the connectedness of the vascular network is an important step towards the characterization of the complete vascular tree. The retinal vascular tree, from an image interpretation point of view, originates at the optic disc and spreads out over the retina. The tree bifurcates and the vessels also cross each other. The points where this happens form the key to determining the connectedness of the complete tree. We present a supervised method to detect the bifurcations and crossing points of the vasculature of the retina. The method uses features extracted from the vasculature as well as the image in a location regression approach to find those locations of the segmented vascular tree where the bifurcation or crossing occurs (from here, POI, points of interest). We evaluate the method on the publicly available DRIVE database in which an ophthalmologist has marked the POI.
Adaptive fuzzy post-filtering for highly compressed video (2005)

This paper presents a newly developed adaptive fuzzy post-filter for removing blocking and ringing artifacts in the highly compressed images and videos. The proposed post-filter adoptively adjusts its filtering window size and the spread parameter in the fuzzy membership function according to the variance value in an edge map. The post-filtering operation is directly applied to the classified edge blocks in the image under the guidance of the edge map, while keeping smooth and textured blocks unchanged. The experimental results demonstrate that the proposed method possesses a good edge preserving property and can maximally remove coding artifacts. Compared with our previous method, the proposed post-filter achieves better objective and subjective quality and further reduces computational complexity.
Self-tolerance curtails the B cell repertoire to microbial epitopes (2019)

Immunological tolerance removes or inactivates self-reactive B cells, including those that also recognize cross-reactive foreign antigens. Whereas a few microbial pathogens exploit these "holes" in the B cell repertoire by mimicking host antigens to evade immune surveillance, the extent to which tolerance reduces the B cell repertoire to foreign antigens is unknown. Here, we use single-cell cultures to determine the repertoires of human B cell antigen receptors (BCRs) before (transitional B cells) and after (mature B cells) the second B cell tolerance checkpoint in both healthy donors and in patients with systemic lupus erythematosus (SLE) . In healthy donors, the majority (~70%) of transitional B cells that recognize foreign antigens also bind human self-antigens (foreign+self), and peripheral tolerance halves the frequency of foreign+self-reactive mature B cells. In contrast, in SLE patients who are defective in the second tolerance checkpoint, frequencies of foreign+self-reactive B cells remain unchanged during maturation of transitional to mature B cells. Patterns of foreign+self-reactivity among mature B cells from healthy donors differ from those of SLE patients. We propose that immune tolerance significantly reduces the scope of the BCR repertoire to microbial pathogens and that cross-reactivity between foreign and self epitopes may be more common than previously appreciated.
Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration (2016)

Long non-coding RNAs (lncRNAs) represent the largest and most diverse class of non-coding RNAs, comprising almost 16,000 currently annotated transcripts in human and 10,000 in mouse. Here, we investigated the role of lncRNAs in mammary tumors by performing RNA-seq on tumor sections and organoids derived from MMTV-PyMT and MMTV-Neu-NDL mice. We identified several hundred lncRNAs that were overexpressed compared to normal mammary epithelium. Among these potentially oncogenic lncRNAs we prioritized a subset as Mammary Tumor Associated RNAs (MaTARs) and determined their human counterparts, hMaTARs. To functionally validate the role of MaTARs, we performed antisense knockdown and observed reduced cell proliferation, invasion, and/or organoid branching in a cancer-specific context. Assessing the expression of hMaTARs in human breast tumors revealed that 19 hMaTARs are significantly upregulated and many of these correlate with breast cancer subtype and/or hormone receptor status, indicating potential clinical relevance.
ChemInform Abstract: (Rh(η4‐((η5‐C5H4)OCH2CH2P(C6H5)2)2Fe))BF4: An Olefin Hydrogenation Catalyst and the First Rhodium(I) cis‐Phosphine‐cis‐ Ether Complex Characterized by Single‐Crystal X‐Ray Diffraction Methods. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A MODEL FOR UNDERSTANDING ONLINE COMMUNITIES (2008)

This paper proposes a holistic model for understanding online communities. According to the model, the technological basis of an online community is the community service and external tools, which features are used by members for participating to the community. The activities of participation are organized into two categories called content and people. The content category consists of activities between a community member and digital content. The people category contains interactions between members of the community. The model also defines elements that directly regulate, or more subtly influence participation. Such elements include policy, privacy, trust, motivation, and roles. According to the model, one outcome of participation is the way a member’s identity gets constructed and defined. The model can be used to compose questions for describing, comparing, and analyzing online communities, and as support for community design.
RAV-Like1Maintains Brassinosteroid Homeostasis via the Coordinated Activation ofBRI1and Biosynthetic Genes in Rice (2010)

Temporal and spatial variation in the levels of and sensitivity to hormones are essential for the development of higher organisms. Traditionally, end-product feedback regulation has been considered as the key mechanism for the achievement of cellular homeostasis. Brassinosteroids (BRs) are plant steroid hormones that are perceived by the cell surface receptor kinase Brassinosteroid Insensitive1. Binding of these hormones to the receptor activates BR signaling and eventually suppresses BR synthesis. This report shows that RAVL1 regulates the expression of the BR receptor. Furthermore, RAVL1 is also required for the expression of the BR biosynthetic genes D2, D11, and BRD1 that are subject to BR negative feedback. Activation by RAVL1 was coordinated via E-box cis-elements in the promoters of the receptor and biosynthetic genes. Also, RAVL1 is necessary for the response of these genes to changes in cellular BR homeostasis. Genetic evidence is presented to strengthen the observation that the primary action of RAVL1 mediates the expression of genes involved in BR signaling and biosynthesis. This study thus describes a regulatory circuit modulating the homeostasis of BR in which RAVL1 ensures the basal activity of both the signaling and the biosynthetic pathways.
The antitumor activity of alternating electric fields (TTFields) in combination with immune checkpoint inhibitors. (2016)

e14570 Background: Tumor Treating Fields (TTFields) are an effective anti-neoplastic treatment modality delivered via application of low intensity, intermediate frequency, alternating electric fields. This therapy is approved for the treatment of patients with glioblastoma. Previous investigations have shown that some of the outcomes of mitosis under TTFields application include abnormal chromosome segregation and ER stress which trigger different forms of cell death. In this study we evaluated whether TTFields induced cancer cell death can be perceived as immunogenic by the immune system, and explored the possibility of combining TTFields with immune-modulating drugs. Methods: Murine Lewis lung carcinoma (LLC) and ovarian surface epithelial (MOSE) cells were treated with TTFields using the inovitro system. The exposure of calreticulin (CRT) on the surface of treated cells was evaluated using flow cytometry. HMGB1 secretion was measured using ELISA assay. For in-vivo experiments, mice were implanted with LLC cells, and treated with TTFields, anti-PD-1 or combination of the two modalities. Changes in tumor volume were monitored and flow cytometry analysis was performed for phenotypic characterization of tumor infiltrating immune cells. Results: We demonstrate that application of TTFields leads to surface exposure of CRT and also promotes release of HMGB1. In vivo, the combined treatment of TTFields and anti-PD-1 led to a significant decrease in tumor volume compared to control group and to animals treated with anti-PD-1 alone. Significant increase in CD45+ tumor infiltrating cells was observed in the TTFields+anti-PD-1 combination treatment group. This cell population demonstrated a significant upregulation of PD-L1 expression on the cell surface. Specifically, this upregulation was observed in both F4/80+CD11b+ cells and CD11c+ cells whereas no effect on the infiltration pattern of these immune cell populations was noted. Conclusions: Our results demonstrate that TTFields application potentiates immunogenic cell death in cancer cells and that combining TTFields with specific immunotherapies such as anti-PD-1 might achieve tumor control by further enhancing antitumor immunity.
Anticancer activity of the supercritical extract of Brazilian green propolis and its active component, artepillinï¿½C: Bioinformatics and experimental analyses of its mechanisms of action (2018)

Propolis, a resinous substance collected by honeybees by mixing their saliva with plant sources, including tree bark and leaves and then mixed with secreted beeswax, possesses a variety of bioactivities. Whereas caffeic acid phenethyl ester (CAPE) has been recognized as a major bioactive ingredient in New Zealand propolis, Brazilian green propolis, on the other hand, possesses artepillin C (ARC). In this study, we report that, similar to CAPE, ARC docks into and abrogates mortalin-p53 complexes, causing the activation of p53 and the growth arrest of cancer cells. Cell viability assays using ARC and green propolis-supercritical extract (GPSE) revealed higher cytotoxicity in the latter, supported by nuclear translocation and the activation of p53. Furthermore, in vivo tumor suppression assays using nude mice, we found that GPSE and its conjugate with γ cyclodextrin (γCD) possessed more potent anticancer activity than purified ARC. GPSE‑γCD may thus be recommended as a natural, effective and economic anticancer amalgam.
A Valleytronic Diamond Transistor: Electrostatic Control of Valley Currents and Charge-State Manipulation of NV Centers (2020)

The valley degree of freedom in many-valley semiconductors provides a new paradigm for storing and processing information in valleytronic and quantum-computing applications. Achieving practical devices requires all-electric control of long-lived valley-polarized states, without the use of strong external magnetic fields. Because of the extreme strength of the carbon-carbon bond, diamond possesses exceptionally stable valley states that provide a useful platform for valleytronic devices. Using ultrapure single-crystalline diamond, we demonstrate electrostatic control of valley currents in a dual-gate field-effect transistor, where the electrons are generated with a short ultraviolet pulse. The charge current and the valley current measured at the receiving electrodes are controlled separately by varying the gate voltages. We propose a model to interpret experimental data, based on drift-diffusion equations coupled through rate terms, with the rates computed by microscopic Monte Carlo simulations. As an application, we demonstrate valley-current charge-state modulation of nitrogen-vacancy centers.
High‐Temperature Interlaminar Tension Test Method Development for Ceramic Matrix Composites (2012)

This chapter contains sections titled: Introduction Experimental Procedures Experimental Results and Discussion Conclusion Acknowledgements
On Enabling Sustainable Edge Computing with Renewable Energy Resources (2018)

The emergent paradigm of edge computing advocates that computational and storage resources can be extended to the edge of the network so that the impact of data transmission latency over the Internet can be effectively reduced for time-constrained Internet of Things applications. With the widespread deployment of edge computing devices, the energy demand of these devices has increased and started to become a noticeable issue for the suitable development of urban systems. In this article, we propose a unified energy management framework for enabling a sustainable edge computing paradigm with distributed renewable energy resources. This framework supports cooperation between the energy supply system and the edge computing system so that renewable energy can be fully utilized while offering improved quality of service for time-constrained IoT applications. A prototype system is also implemented by using microgrid (solar-wind hybrid energy system) and edge computing devices together. The experiment results demonstrate that renewable energy is fully capable of supporting the reliable running of edge computing devices in the prototype system during most (94.8 percent) of the experimental period when our proposed framework was employed.
Temozolomide Induces the Production of Epidermal Growth Factor to Regulate MDR1 Expression in Glioblastoma Cells (2014)

Glioblastoma multiforme (GBM) commonly resists the frontline chemotherapy treatment temozolomide. The multidrug resistance gene (MDR1) and its protein, P-glycoprotein (P-gp), are associated with chemoresistance. This study investigated the mechanisms underlying MDR1-mediated resistance by GBM to temozolomide. P-gp trafficking was studied by flow cytometry and Western blot analysis. MDR1 expression was analyzed by real-time PCR and reporter gene assays. AP-1 interaction with MDR1 was studied by chromatin immunoprecipitation assay. EGF production was analyzed by ELISA, EGFR signaling was determined by Western blot analysis, and in vivo response to erlotinib and/or temozolomide was studied in nude mice. During the early phase of temozolomide treatment, intracellular P-gp was trafficked to the cell membrane, followed by conformational change into active P-gp. At the later phase, gene transcription of MDR1 was induced by temozolomide-mediated production of EGF. EGF activated ERK1/2-JNK-AP-1 cofactors (c-jun and c-fos). An inhibitor of EGFR kinase (erlotinib) given to nude mice with GBM prevented temozolomide-induced resistance. The results identified an essential role for activated EGFR in the resistance of GBM to temozolomide. Temozolomide resistance occurred through a biphasic response; first, by a conformational change in P-gp into the active form and, second, by releasing EGF, which caused autocrine stimulation of GBM cells to induce MDR1. Pharmacologic inhibition of EGFR kinase blunted the ability of GBM cells to resist temozolomide. These findings may explain reports on the common occurrence of mutant EGFR (EGFRvIII) and EGFR expansion in the resistance of GBM cells.
Co-administration of Favipiravir and the Remdesivir Metabolite GS-441524 Effectively Reduces SARS-CoV-2 Replication in the Lungs of the Syrian Hamster Model (2022)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide since December 2019, causing coronavirus disease 2019 (COVID-19). Although vaccines for this virus have been developed rapidly, repurposing drugs approved to treat other diseases remains an invaluable treatment strategy. Here, we evaluated the inhibitory effects of drugs on SARS-CoV-2 replication in a hamster infection model and in <i>in vitro</i> assays. Favipiravir significantly suppressed virus replication in hamster lungs. Remdesivir inhibited virus replication <i>in vitro</i>, but was not effective in the hamster model. However, GS-441524, a metabolite of remdesivir, effectively suppressed virus replication in hamsters. Co-administration of favipiravir and GS-441524 more efficiently reduced virus load in hamster lungs than did single administration of either drug for both the prophylactic and therapeutic regimens; prophylactic co-administration also efficiently inhibited lung inflammation in the infected animals. Furthermore, pretreatment of hamsters with favipiravir and GS-441524 effectively protected them from virus transmission via respiratory droplets upon exposure to infected hamsters. Repurposing and co-administration of antiviral drugs may help combat COVID-19. <b>IMPORTANCE</b> During a pandemic, repurposing drugs that are approved for other diseases is a quick and realistic treatment option. In this study, we found that co-administration of favipiravir and the remdesivir metabolite GS-441524 more effectively blocked SARS-CoV-2 replication in the lungs of Syrian hamsters than either favipiravir or GS-441524 alone as part of a prophylactic or therapeutic regimen. Prophylactic co-administration also reduced the severity of lung inflammation. Moreover, co-administration of these drugs to naive hamsters efficiently protected them from airborne transmission of the virus from infected animals. Since both drugs are nucleotide analogs that interfere with the RNA-dependent RNA polymerases of many RNA viruses, these findings may also help encourage co-administration of antivirals to combat future pandemics.
Protective Potential of Antioxidant Enzymes as Vaccines for Schistosomiasis in a Non-Human Primate Model (2015)

Schistosomiasis remains a major cause of morbidity in the world. The challenge today is not so much in the clinical management of individual patients, but rather in population-based control of transmission in endemic areas. Despite recent large-scale efforts, such as integrated control programs aimed at limiting schistosomiasis by improving education and sanitation, molluscicide treatment programs and chemotherapy with praziquantel, there has only been limited success. There is an urgent need for complementary approaches, such as vaccines. We demonstrated previously that anti-oxidant enzymes, such as Cu-Zn superoxide dismutase (SOD) and glutathione S peroxidase (GPX), when administered as DNA-based vaccines induced significant levels of protection in inbred mice, greater than the target 40% reduction in worm burden compared to controls set as a minimum by the WHO. These results led us to investigate if immunization of non-human primates with antioxidants would stimulate an immune response that could confer protection as a prelude study for human trials. Issues of vaccine toxicity and safety that were difficult to address in mice were also investigated. All baboons in the study were examined clinically throughout the study and no adverse reactions occurred to the immunization. When our outbred baboons were vaccinated with two different formulations of SOD (SmCT-SOD and SmEC-SOD) or one of GPX (SmGPX), they showed a reduction in worm number to varying degrees, when compared with the control group. More pronounced, vaccinated animals showed decreased bloody diarrhea, days of diarrhea, and egg excretion (transmission), as well as reduction of eggs in the liver tissue and in the large intestine (pathology) compared to controls. Specific IgG antibodies were present in sera after immunizations and 10 weeks after challenge infection compared to controls. Peripheral blood mononuclear cells, mesenteric, and inguinal node cells from vaccinated animals proliferated and produced high levels of cytokines and chemokines in response to crude and recombinant antigens compared with controls. All together, these data demonstrate the potential of antioxidants as a vaccine in a non-human primate model.