gebhart/patrepeval huggingface dataset:
Fatty acid binding protein 4 is a target of VEGF and a regulator of cell proliferation in endothelial cells (2009)

Fatty acid binding protein 4 (FABP4) plays an important role in maintaining glucose and lipid homeostasis. FABP4 has been primarily regarded as an adipocyte- and macrophage-specific protein, but recent studies suggest that it may be more widely expressed. We found strong FABP4 expression in the endothelial cells (ECs) of capillaries and small veins in several mouse and human tissues, including the heart and kidney. FABP4 was also detected in the ECs of mature human placental vessels and infantile hemangiomas, the most common tumor of infancy and ECs. In most of these cases, FABP4 was detected in both the nucleus and cytoplasm. FABP4 mRNA and protein levels were significantly induced in cultured ECs by VEGF-A and bFGF treatment. The effect of VEGF-A on FABP4 expression was inhibited by chemical inhibition or short-hairpin (sh) RNA-mediated knockdown of VEGF-receptor-2 (R2), whereas the VEGFR1 agonists, placental growth factors 1 and 2, had no effect on FABP4 expression. Knockdown of FABP4 in ECs significantly reduced proliferation both under baseline conditions and in response to VEGF and bFGF. Thus, FABP4 emerged as a novel target of the VEGF/VEGFR2 pathway and a positive regulator of cell proliferation in ECs.
Inhibition of Wnt Signaling by Exogenous Mfrzbl Protein Affects Molar Tooth Size (2000)

Wnt extracellular signaling molecules have essential roles as regulators of cell proliferation, migration, differentiation, and in epithelial-mesenchymal interactions involved in tissue morphogenesis. Frizzled integral membrane proteins have been shown to function as receptors for Wnt signaling molecules. Vertebrates also produce secreted proteins related to Frizzled receptors, Frizzled-related proteins (FRPs), which contain the cysteine-rich domain of Frizzleds and appear to function as Wnt antagonists. Tooth development is regulated by a reciprocal series of epithelial-mesenchymal interactions, and many Wnt signaling pathway genes are expressed in the developing tooth at these sites. Here we report the expression of one FRP gene, Mfrzb1, in the rostral mesenchyme of the mandibular primordium. Using explant cultures, we show that expression of Mfrzb1 in the mandibular mesenchyme is under the control of signals derived from the overlying epithelium. Bead implantation experiments in vitro show that FGF8 induces Mfrzb1 expression, whereas BMP4 and SHH proteins have no effect. We studied the effect of ectopic MFrzb1 protein on the developing tooth germs by transplanting explants treated with Mfrzb1 protein into renal capsules, and found it to retard tooth development. This suggests that Wnt signaling is required early in tooth germ formation and that interference with signaling via addition of an antagonist results in retarded development and formation of smaller teeth.
Reversal mechanisms in perpendicularly magnetized nanostructures (2008)

We demonstrate that magnetic reversal in perpendicularly magnetized nanostructures is highly dependent on the nature and condition of the edges. To understand the impact of edge damage, we compare nanostructures created by ion milling to those prepared on prepatterned substrates. The size- and temperature-dependent reversal properties of 25 nm--$1\text{ }\ensuremath{\mu}\text{m}$ diameter nanodots show that reversal in prepatterned nanostructures is controlled by nucleation within the interior, whereas ion milling results in an edge nucleation process with an unpredicted temperature dependence of the reversal field.
LHCII Populations in Different Quenching States Are Present in the Thylakoid Membranes in a Ratio that Depends on the Light Conditions (2015)

LHCII is the major antenna complex of plants and algae, where it is involved in light harvesting and photoprotection. Its properties have been extensively studied in vitro, after isolation of the pigment-protein complex from the membranes, but are these properties representative for LHCII in the thylakoid membrane? In this work, we have studied LHCII in the cells of the green alga C. reinhardtii acclimated to different light conditions in the absence of the other components of the photosynthetic apparatus. We show that LHCII exists in the membranes in different fluorescence quenching states, all having a shorter excited-state lifetime than isolated LHCII in detergent. The ratio between these populations depends on the light conditions, indicating that the light is able to regulate the properties of the complexes in the membrane.
Quantifying Metabolic Heterogeneity in Head and Neck Tumors in Real Time: 2-DG Uptake Is Highest in Hypoxic Tumor Regions (2014)

Hypoxia is associated with increased intratumoral metabolic heterogeneity. (18)F-FDG PET scans may be used to stratify patients according to the metabolic heterogeneity within their tumors, which could be an indicator of prognosis.
Iterative Receiver Design (2007)

Iterative processing is an important technique with numerous applications. Exploiting the power of factor graphs, this detailed survey provides a general framework for systematically developing iterative algorithms for digital receivers, and highlights connections between important algorithms. Starting with basic concepts in digital communications, progressively more complex ideas are presented and integrated resulting in the development of cutting-edge algorithms for iterative receivers. Real-world applications are covered in detail, including decoding for turbo and LDPC codes, and detection for multi-antenna and multi-user systems. This accessible framework will allow the reader to apply factor graphs to practical problems, leading to the design of new algorithms in applications beyond digital receivers. With many examples and algorithms in pseudo-code, this book is an invaluable resource for graduate students and researchers in electrical engineering and computer science, and for practitioners in the communications industry. Additional resources for this title are available online at www.cambridge.org/9780521873154.
Fast parallel skew and prefix‐doubling suffix array construction on the GPU (2016)

Summary Suffix arrays are fundamental full‐text index data structures of importance to a broad spectrum of applications in such fields as bioinformatics, Burrows–Wheeler transform‐based lossless data compression, and information retrieval. In this work, we propose and implement two massively parallel approaches on the graphics processing unit (GPU) based on two classes of suffix array construction algorithms. The first, parallel skew , makes algorithmic improvements to the previous work of Deo and Keely to achieve a speedup of 1.45x over their work. The second, a hybrid skew and prefix‐doubling implementation, is the first of its kind on the GPU and achieves a speedup of 2.3–4.4x over Osipov's prefix‐doubling and 2.4–7.9x over our skew implementation on large datasets. Our implementations rely on two efficient parallel primitives, a merge and a segmented sort. We theoretically analyze the two formulations of suffix array construction algorithms and show performance comparisons on a large variety of practical inputs. We conclude that, with the novel use of our efficient segmented sort, prefix‐doubling is more competitive than skew on the GPU. We also demonstrate the effectiveness of our methods in our implementations of the Burrows‐Wheeler transform and in a parallel full‐text, minute‐space‐index for pattern searching. Copyright © 2016 John Wiley & Sons, Ltd.
Inhibition of Interleukin‐6/glycoprotein 130 signalling by Bazedoxifene ameliorates cardiac remodelling in pressure overload mice (2020)

The role of IL-6 signalling in hypertensive heart disease and its sequelae is controversial. Our group demonstrated that Bazedoxifene suppressed IL-6/gp130 signalling in cancer cells but its effect on myocardial pathology induced by pressure overload is still unknown. We explored whether Bazedoxifene could confer benefits in wild-type C57BL/6J mice suffering from transverse aortic constriction (TAC) and the potential mechanisms in H9c2 myoblasts. Mice were randomized into three groups (Sham, TAC, TAC+Bazedoxifene, n = 10). Morphological and histological observations suggested TAC aggravated myocardial remodelling while long-term intake of Bazedoxifene (5 mg/kg, intragastric) attenuated pressure overload-induced pathology. Echocardiographic results indicated Bazedoxifene rescued cardiac function in part. We found Bazedoxifene decreased the mRNA expression of IL-6, MMP2, Col1A1, Col3A1 and periostin in murine hearts after 8-week surgery. By Western blot detection, we found Bazedoxifene exhibited an inhibition of STAT3 activation in mice three hours and 8 weeks after TAC. Acute TAC stress (3 hours) led to down-regulated ratio of LC3-Ⅱ/LC3-Ⅰ, while in mice after long-term (8 weeks) TAC this ratio becomes higher than that in Sham mice. Bazedoxifene inverted the autophagic alteration induced by TAC at both two time-points. In H9c2 myoblasts, Bazedoxifene suppressed the IL-6-induced STAT3 activation. Moreover, IL-6 reduced the ratio of LC3-Ⅱ/LC3-Ⅰ, promoted P62 expression but Bazedoxifene reversed both changes in H9c2 cells. Our data suggested Bazedoxifene inhibited IL-6/gp130 signalling and protected against cardiac remodelling together with function deterioration in TAC mice.
The role of superantigens in human diseases: therapeutic implications for the treatment of skin diseases (1998)

Although it is well established that immune mechanisms contribute to the pathogenesis of chronic inflammatory skin diseases such as atopic dermatitis (AD) and psoriasis, the actual events that trigger the immunological pathways resulting in these skin diseases are not well understood. Colonization and infection with Staphylococcus aureus and streptococci has been reported to exacerbate AD and psoriasis. Recent studies demonstrating that bacterial toxins can act as superantigens provide mechanism(s) by which S. aureus and streptococci could mediate an inflammatory skin lesion that consists predominantly of activated T-cells and monocytes. This review will explore the diverse mechanisms by which bacterial superantigens can induce skin inflammation following systemic or local infection. These observations provide a new direction for the development of novel approaches for the treatment of skin inflammation.
Using the Simplicity Cycle in Model Building (2009)

Computer based Decision Support Tools or Systems (DST or DSS) have been used inagriculture and natural resource management for over 30 years. However their uptake has been patchy, and reviews in both fields arrive at a similar set of explanations; 1) Absence of market research to establish need and target audience; 2) Failure to clearly define the problem in participation with users; 3) Their complexity; 4) Failure to acknowledge the qualitative and subjective processes common to all problem solving; 5) Making decisions for the user instead of providing information to help them make their own (e.g. optimising); 6) Use of opaque logic; 7) Failure to provide intermediaries to facilitate their use by managers. An additional impediment identified for agricultural DSS is that of scale, where those that focus on whole of system (e.g. farm profitability) rather than operational issues (e.g. nutrient application in cropping) have poorer uptake. While this question of scale is more difficult to avoid in natural resource management, it is related to the issue of complexity and has implications for ease of use and likelihood of uptake.The Landscape Logic research hub (www.landscapelogic.org.au) was set up todevelop decision support systems with environmental managers who haveresponsibility for investing public funds to improve water quality and vegetation condition. Its approach to DDS development is based on four principles, adopted in an attempt to avoid the shortcomings identified above; 1)Participation of end users in problem definition and model testing; 2) UsingBayesian Decision Networks as the modelling framework to establish a transparent logic and incorporate quantitative and qualitative information; 3)Using the Simplicity Cycle to guide model development 4) Training and licensing third party intermediaries to facilitate future use. A companion paper (Pollino, Lefroy and Jakeman, this volume) describes the first two features.This paper concentrates on the application of the simplicity cycle to model building. This process starts from a position of low utility and low complexity with naively simple conceptual models. It then moves through several iterations of high complexity and low utility (confused complexity) until it arrives at a sufficient level of complexity to adequately represent the system (requisite complexity). The ultimate aim is to arrive at a state of low complexity and high utility (informed simplicity) by progressively discarding drivers, nodes and links to which the systems is least sensitive.
The integrase interactor 1 (INI1) proteins facilitate Tat-mediated human immunodeficiency virus type 1 transcription (2006)

Integration of human immunodeficiency virus type 1 (HIV-1) into the host genome is catalyzed by the viral integrase (IN) and preferentially occurs within transcriptionally active genes. During the early phase of HIV-1 infection, the incoming viral preintegration complex (PIC) recruits the integrase interactor 1 (INI1)/hSNF5, a chromatin remodeling factor which directly binds to HIV-1 IN. The impact of this event on viral replication is so far unknown, although it has been hypothesized that it could tether the preintegration complex to transcriptionally active genes, thus contributing to the bias of HIV integration for these regions of the genome. Here, we demonstrate that while INI1 is dispensable for HIV-1 transduction, it can facilitate HIV-1 transcription by enhancing Tat function. INI1 bound to Tat and both the repeat (Rpt) 1 and Rpt 2 domains of INI1 were required for efficient activation of Tat-mediated transcription. These results suggest that the incoming PICs might recruit INI1 to facilitate proviral transcription.
Fast rate distortion optimized quantization for HEVC (2015)

As the new generation video coding standard, the High Efficiency Video Coding (HEVC) achieves significantly better coding efficiency than existing video coding standards, which is however at the cost of a much higher computational complexity. Rate-Distortion Optimized Quantization (RDOQ) is one of the powerful coding tools employed in HEVC to pursue high coding efficiency. Nevertheless, RDOQ requires an exhaustive search over multiple candidates to determine the optimal quantized level through Rate-Distortion Optimization (RDO), which leads to considerable complexity in practice. This paper addresses this issue from a new point of view and presents a fast RDOQ scheme for transformed DCT coefficients quantization in HEVC. More specifically, we first proposed a RDOQ call removal algorithm which can effectively remove the redundant RDOQ calls and thus speed up the RDOQ process. Secondly, an all-zero block-based RDOQ skip algorithm is developed to skip unnecessary RDOQ. Compared to HEVC reference software, the proposed algorithms can save on average 34% of the RDOQ time with only slight performance degradation. Besides, our proposed algorithms can be incorporated with existing fast RDOQ algorithms to further improve the encoding efficiency.
In situ characterization techniques for monitoring and control of VPE growth of Hg<sub>1-x</sub>Cd<sub>x</sub>Te (1993)

In situ diagnostic techniques are broadly divided into two categories, those involving an electron probe or reflected beam and those relying just on photon beams. The former, such as RHEED, XPS, AES and UPS, can be used in MBE monitoring but are not suitable for the high-pressure environment of MOVPE. Optical diagnostic techniques such as ellipsometry, laser reflectometry, quasielectric light scattering, reflection difference spectroscopy (RDS) and infrared reflection-absorption spectroscopy (IRRAS) can be used as an in situ monitor in both UHV and high-pressure growth chambers. These are compared with the electron beam techniques and some analogues are established in terms of the properties of the growing films. The in situ monitoring of MCT growth is helping to improve layer quality and reproducibility. Some specific examples are discussed, including the potential for in situ feedback control.
A gas monitoring system for ethylene oxide sterilizers with constant sample flow through a microwave cavity spectrometer (1993)

This paper reports a measurement system for monitoring the gas concentrations of ethylene oxide (EO) within sterilizers. It samples gas from the sterilizer chamber at a constant flow into a microwave cavity spectrometer. The pressure in the cavity of the spectrometer is linearly proportional to that in the sterilizer chamber, hence the partial pressure (i.e. gas concentration) of the EO gas is linearly proportional to that in the chamber. Measurement of the gas concentration in the chamber can therefore take place without the need to monitor and interpret the chamber pressure. As a consequence the reliability of the sterilization process may be improved, thus enabling a reduction in the in-chamber concentration of EO during sterilization and, hence, EO residues. The microwave cavity spectrometer operates under conditions of power saturation, and there is a good linear correlation between the output signal and the concentration of EO in the gas cell (to within a standard error of 4%).
A Structural Requirement for Processing the Cardiac K+ Channel KCNQ1 (2004)

Normal membrane protein function requires trafficking from the endoplasmic reticulum. Here, we studied processing of the KCNQ1 channel mutated in LQT1, the commonest form of the long QT syndrome. Serial C terminus truncations identified a small region (amino acids (aa) 610-620) required for normal cell surface expression. Non-trafficked truncations assembled as tetramers but were nevertheless retained in the endoplasmic reticulum. Further mutagenesis did not identify specific residues mediating channel processing; cell surface expression was preserved with the mutation of known trafficking motifs in the channel and with alanine scanning across aa 610-620. Structural prediction algorithms place aa 610-620 at the C-terminal end of an alpha-helix (aa 586-618) that includes a leucine zipper and is part of a coiled coil. Mutants disrupting the leucine zipper but preserving the predicted coiled coil reached the cell surface, whereas those disrupting the coil did not. These data suggest that specific protein-protein interactions are required for normal channel processing. Further biochemical studies ruled out three candidate proteins, namely KCNE1, yotiao, and KCNQ1 itself, as effectors of this coiled coil-mediated trafficking. Four LQT1 mutations within this helix generated little or no current and were not expressed on the cell surface, whereas LQT1 mutations in adjacent residues, which produce a milder clinical phenotype, generate only slightly reduced current and are expressed on the cell surface. These data suggest that mutations within this domain cause human disease by interfering with normal channel processing. More generally, we have identified a domain whose structural integrity is required for normal surface expression of the KCNQ1 channel.
Electrotransfer parameters as a tool for controlled and targeted gene expression in skin (2016)

Skin is an attractive target for gene electrotransfer. It consists of different cell types that can be transfected, leading to various responses to gene electrotransfer. We demonstrate that these responses could be controlled by selecting the appropriate electrotransfer parameters. Specifically, the application of low or high electric pulses, applied by multi-electrode array, provided the possibility to control the depth of the transfection in the skin, the duration and the level of gene expression, as well as the local or systemic distribution of the transgene. The influence of electric pulse type was first studied using a plasmid encoding a reporter gene (DsRed). Then, plasmids encoding therapeutic genes (IL-12, shRNA against endoglin, shRNA against melanoma cell adhesion molecule) were used, and their effects on wound healing and cutaneous B16F10 melanoma tumors were investigated. The high-voltage pulses resulted in gene expression that was restricted to superficial skin layers and induced a local response. In contrast, the low-voltage electric pulses promoted transfection into the deeper skin layers, resulting in prolonged gene expression and higher transgene production, possibly with systemic distribution. Therefore, in the translation into the clinics, it will be of the utmost importance to adjust the electrotransfer parameters for different therapeutic approaches and specific mode of action of the therapeutic gene.
I Am Alice, I Was in Wonderland: Secure Location Proof Generation and Verification Protocol (2016)

In recent years, the proliferation of wireless devices has contributed to the emergence of new set of applications termed as Location Based Services (LBS). LBS provide privileges to mobile users based on their proximity to a facility. In order to gain benefits, users may lie or falsely claim their location. Hence, it is essential to verify the legitimacy of users. In this paper, we propose our novel solution for generating location proof for mobile users and verification of the location claim by application services. Our protocol exploits unique Wi-Fi signal characteristics and employs an information theoretically secure fuzzy vault scheme. We provide a detailed theoretical and experimental evaluation of our protocol. Our solution is faster by an order of magnitude, and the performance of our scheme is independent of the location tag size and distance between the mobile user and location proof provider compared to the state-of-the-art.
Inter view motion vector prediction in multiview HEVC (2014)

In multiview coding, motion information of different views forming the multiview video is correlated. The multiview extension of High Efficiency Video Coding (MV-HEVC) that is currently under development is defined to allow multi-view coding with minimal changes to HEVC. This is realized by simply adding the reconstructed base view picture to the reference picture list of the dependent views. MV-HEVC specification is restricted from low-level operations with motion information, thus redundancy in motion information between views is not utilized. This paper proposes to use the temporal motion vector prediction mechanism of HEVC to enable the prediction of motion vectors from the inter-view reference picture; similar to the concept of Motion Field Mapping mechanism in the scalable extension of HEVC. In order to compensate for the disparity, it is also proposed to signal a global disparity value for motion field adjustment. Global disparity is estimated at the encoder side for each slice and signaled to the decoder side at the slice header. Simulations conducted in the MV-HEVC configuration of 3D-HTM v6.0 show that the proposed method brings 1.1% of dBR for view 1 and 0.8% for view 2 which results in 0.6% gain on average of all views.