gebhart/patrepeval huggingface dataset:
Sphingosine‐1‐phosphate signalling induces the production of Lcn‐2 by macrophages to promote kidney regeneration (2011)

Inflammatory reactions are initiated to eliminate pathogens, but also to promote repair of damaged tissue after acute inflammation is terminated. In this regard, macrophages play a prominent role during induction as well as resolution of inflammation and injury in various organs including the kidney. The present study describes a mechanism for renal tissue regeneration after ischaemia/reperfusion injury. Following injury, apoptotic cell-derived sphingosine-1-phosphate (S1P) or exogenously administered sphingosine analogue FTY720 activates macrophages to support the proliferation and healing of renal epithelium, once inflammatory conditions are terminated. Both suppression of inflammation and renal regeneration might require S1P receptor 3 (S1P3) signalling and downstream release of neutrophil gelatinase-associated lipocalin (NGAL/Lcn-2) from macrophages. Overall, our data point to a macrophage-dependent S1P-S1P3-Lcn-2 axis that might be beneficial for restoration of kidney function after an ischaemic insult.
Three-dimensional H-1 MR spectroscopic imaging of the in situ human prostate with high (0.24-0.7-cm3) spatial resolution. (1996)

These results suggest that a 3D MRSI examination added to a clinical MR imaging examination may help define the presence and spatial extent of prostate cancer.
WiFi-XL: Extending WiFi to Wide Areas in White Spaces (2014)

Due to its superior propagation characteristics, white spaces has the potential to enable license-free wireless wide-area networks (WWAN). However, we show that using standard WiFi in white spaces will not deliver adequate capacity or coverage because of two characteristics unique to WWANs, namely, channel trichotomy which greatly increases number of interferers and sub-noise communication support, crucial for wide coverage. In this paper, we design, implement and evaluate WiFi-XL – a white space WWAN that extends WiFi-like spectrum sharing to wide areas. WiFi-XL comprises two novel design elements: idle-quantum hopping that allows nodes to minimize number of interferers, and code-domain contention that enables range extension through efficient sub-noise communication support. We demonstrate the effectiveness of these design elements using simulations and experiments in wide-area settings.
Staphylococcus epidermidis biofilms: importance and implications (2001)

The coagulase-negative staphylococci and, in particular, Staphylococcus epidermidis, have emerged as major nosocomial pathogens associated with infections of implanted medical devices. These organisms, which are among the most prevalent bacteria of the human skin and mucous membrane microflora, present unique problems in the diagnosis and treatment of infections involving biofilm formation on implanted biomaterials. Epidemiological data that address whether invasive S. epidermidis strains can be traced to commensal organisms or an endemic occurrence of distinct strains with enhanced virulence have important implications for the implementation of appropriate infection control measures. An extracellular polysaccharide adhesin represents a key virulence determinant in S. epidermidis and is required for biofilm formation. Production of this adhesin, which is encoded by the ica operon, is subject to phase variable regulation (ON <---> OFF switching). Recent advances in understanding the molecular events controlling polysaccharide adhesin synthesis and the potential clinical implications of its phase variable regulation are outlined. Further research in this area may contribute to the development of novel strategies for therapeutic intervention. Finally, in addition to antibiotic prophylaxis, preventive strategies to control S. epidermidis medical device-related infections are focusing on the development of improved biomaterials and physical electrical barriers to impede bacterial colonisation.
Single‐Crystal Semiconductor Wires Integrated into Microstructured Optical Fibers (2008)

Single-crystal silicon wires are grown within the pores of microstructured optical fibers via a high-pressure fluid-liquid-solid approach. Precise spatial organization of single crystal semiconductor wires offers a flexible alternative approach to the self-assembly or lithographic techniques often used for patterning wires for electronics and photonics. This will enable new composite materials that allow for cooperative photonic and electronic phenomena. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200701569_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
An adaptive immune algorithm based gravimetric fluid dispensing machine (2011)

A dispensing system is used in a materials-mixing plant to provide accurate blend ratios in producing the desired end-use product. The AIS-based (Artificial Immune Systems) fine tuning of dispensing parameters is proposed by optimizing the components of dispensing time and stopping time delay to obtain constant and accurate reading from the precision balance scale. Based on the new dispensing sequence, experimental tests had been carried out using different materials with varying viscosities. The results indicate that the combination of both PWM and AIS techniques would minimize overshoot while exhibiting lower steady-state error and faster response time. These are important in order to overcome the limitations of the conventional volumetric dispensing and manual parameter tuning presently applied in the dispensing system used in the coatings industry.
Osmolyte-Mediated Encapsulation of Proteins inside MS2 Viral Capsids (2012)

The encapsulation of enzymes in nanometer-sized compartments has the potential to enhance and control enzymatic activity, both in vivo and in vitro. Despite this potential, there is little quantitative data on the effect of encapsulation in a well-defined compartment under varying conditions. To gain more insight into these effects, we have characterized two improved methods for the encapsulation of heterologous molecules inside bacteriophage MS2 viral capsids. First, attaching DNA oligomers to a molecule of interest and incubating it with MS2 coat protein dimers yielded reassembled capsids that packaged the tagged molecules. The addition of a protein-stabilizing osmolyte, trimethylamine-N-oxide, significantly increased the yields of reassembly. Second, we found that expressed proteins with genetically encoded negatively charged peptide tags could also induce capsid reassembly, resulting in high yields of reassembled capsids containing the protein. This second method was used to encapsulate alkaline phosphatase tagged with a 16 amino acid peptide. The purified encapsulated enzyme was found to have the same K(m) value and a slightly lower k(cat) value than the free enzyme, indicating that this method of encapsulation had a minimal effect on enzyme kinetics. This method provides a practical and potentially scalable way of studying the complex effects of encapsulating enzymes in protein-based compartments.
Inhibitory diffusible factor IDF45, a G<sub>1</sub> phase inhibitor (1986)

An inhibitory diffusible factor of 45 kDa (IDF45) was isolated from medium conditioned by dense cultures of 3T3 cells. The procedure involved Bio-Gel P150 chromatography and 2 reverse-phase FPLC. After the final step of purification, 60 ng/ml of IDF45 inhibited 50% of alpha-globulin-stimulated DNA synthesis. It was shown that IDF45 acted in the G1 phase of the cell cycle. When added for 8 h in the G1 phase of the cell cycle, it was able to inhibit DNA synthesis in the S phase which followed this G1 phase. Furthermore, IDF45 inhibited the early stimulation of RNA synthesis induced by alpha-globulin.
On a generalization of Blaschke's Rolling Theorem and the smoothing of surfaces (1999)

A generalization of Blaschke's Rolling Theorem for not necessarily convex sets is proved that exhibits an intimate connection between a generalized notion of convexity, various concepts in mathematical morphology and image processing, and a certain smoothness condition. As a consequence a geometric characterization of Serra's regular model is obtained and various problems in image processing arisng from the smoothing of surfaces with Sternberg's rolling ball algorithm are addressed. Copyright © 1999 John Wiley & Sons, Ltd.
Biocompatible, Biodegradable, and Electroactive Polyurethane-Urea Elastomers with Tunable Hydrophilicity for Skeletal Muscle Tissue Engineering (2015)

It remains a challenge to develop electroactive and elastic biomaterials to mimic the elasticity of soft tissue and to regulate the cell behavior during tissue regeneration. We designed and synthesized a series of novel electroactive and biodegradable polyurethane-urea (PUU) copolymers with elastomeric property by combining the properties of polyurethanes and conducting polymers. The electroactive PUU copolymers were synthesized from amine capped aniline trimer (ACAT), dimethylol propionic acid (DMPA), polylactide, and hexamethylene diisocyanate. The electroactivity of the PUU copolymers were studied by UV-vis spectroscopy and cyclic voltammetry. Elasticity and Young's modulus were tailored by the polylactide segment length and ACAT content. Hydrophilicity of the copolymer films was tuned by changing DMPA content and doping of the copolymer. Cytotoxicity of the PUU copolymers was evaluated by mouse C2C12 myoblast cells. The myogenic differentiation of C2C12 myoblasts on copolymer films was also studied by analyzing the morphology of myotubes and relative gene expression during myogenic differentiation. The chemical structure, thermal properties, surface morphology, and processability of the PUU copolymers were characterized by NMR, FT-IR, gel permeation chromatography (GPC), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), and solubility testing, respectively. Those biodegradable electroactive elastic PUU copolymers are promising materials for repair of soft tissues such as skeletal muscle, cardiac muscle, and nerve.
Fully automatic segmentation of heart chambers in cardiac MRI using deep learning (2016)

Cardiac magnetic resonance imaging (MRI) is now routinely being used for the evaluation of the function and structure of the cardiovascular system. Chamber segmentation from cardiac MRI datasets is an essential step for the computation of clinical indices such as ventricular volume, ejection fraction, mass and wall thickness as well as analysis of wall motion abnormality.
CNOT circuit extraction for topologically-constrained quantum memories (2020)

Many physical implementations of quantum computers impose stringent memory constraints in which 2-qubit operations can only be performed between qubits which are nearest neighbours in a lattice or graph structure. Hence, before a computation can be run on such a device, it must be mapped onto the physical architecture. That is, logical qubits must be assigned physical locations in the quantum memory, and the circuit must be replaced by an equivalent one containing only operations between nearest neighbours. In this paper, we give a new technique for quantum circuit mapping (a.k.a. routing), based on Gaussian elimination constrained to certain optimal spanning trees called Steiner trees. We give a reference implementation of the technique for CNOT circuits and show that it significantly out-performs general-purpose routines on CNOT circuits. We then comment on how the technique can be extended straightforwardly to the synthesis of CNOT+Rz circuits and as a modification to a recently-proposed circuit simplification/extraction procedure for generic circuits based on the ZX-calculus.
Water under the Cover: Structures and Thermodynamics of Water Encapsulated by Graphene (2015)

Understanding the phase behaviors of nanoconfined water has driven notable research interests recently. In this work, we examine the structures and thermodynamics of water encapsulated under a graphene cover. We find layered water structures up to ~1000 molecules, which is stabilized by the spatial confinement and pressure induced by the adhesion between graphene cover and substrate. For monolayer encapsulations, we identify both crystalline lattices and defects. Free energy analysis shows that these low- entropy orders are compensated by high formation energies. There exists an order- disorder transition for this condensed phase at ~480-490 K, with a sharp reduction in the number of hydrogen bonds and increase in the entropy. These findings offer fundamental understandings of the encapsulated water, and provide guidance for practical applications with its presence, for example, in the design of nanoelectronic devices.
The ITRS MPU and SOC system drivers: Calibration and implications for design-based equivalent scaling in the roadmap (2014)

The system driver models for microprocessor (MPU) and system-on-chip (SOC) in the International Technology Roadmap for Semiconductors [21] (ITRS) determine the roadmap of underlying technology requirements across devices, patterning, interconnect, test, design and other semiconductor supplier industries. In this paper, we describe several fundamental changes in the ITRS MPU and SOC system driver models as of the recently-released 2013 edition of the roadmap. We first present new A-factor (i.e., layout density) models for the logic and memory components of the MPU and SOC drivers; these updated density models comprehend the industry's shift to FinFET devices below the foundry 20nm node. We also describe updated architectural, total chip area, and total chip power models for the MPU and SOC drivers. Notably, we model the growing uncore portion of MPU products, and the growing presence of graphic processing units (GPUs) and other peripheral cores (PEs) in SOC architectures. The updated SOC architectural model enables more realistic scenario-based power modeling for the SOC driver. The 2013 ITRS update of system driver models embodies extensive calibration with foundry data as well as product structural analysis reports from a leading analysis firm (Chipworks). The model calibration reveals that the industry has contended with a “scaling gap” since 2008, whereby traditional Moore's-Law density scaling of 2× per node has failed due to patterning limitations on layout design, as well as manufacturability and performability challenges of Metal-1 half-pitch (M1HP) scaling. Growing design margins due to reliability, yield, variability, etc. have also contributed to the slowdown of density scaling. We describe how this scaling gap can potentially be compensated if the semiconductor industry urgently pursues design-based equivalent scaling (DES), which substantially changes the area and power model trajectories of MPUs and SOCs in the ITRS System Drivers Chapter. Finally, we note that as a consequence of the updated A-factor, area and power models in the 2013 ITRS, the industry now faces a 20% more daunting power management challenge than had been predicted in the 2011 roadmap.
Roquefortine E, a Diketopiperazine from an Australian Isolate of <i>Gymnoascus </i><i>r</i><i>eessii</i> (2005)

The new isoprenylated diketopiperazine roquefortine E (6) has been isolated from an Australian soil isolate of the ascomycete Gymnoascus reessii. The known fungal metabolite roquefortine C (1) was also recovered as the major antibacterial principle, and all structures were assigned by detailed spectroscopic analysis.
Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects (2022)

RAS mutations prevalent in high-risk leukemia have been linked to relapse and chemotherapy resistance. Efforts to directly target RAS proteins have been largely unsuccessful. However, since RAS-mediated transformation is dependent on signaling through the RAS-related C3 botulinum toxin substrate (RAC) small GTPase, we hypothesized that targeting RAC may be an effective therapeutic approach in RAS mutated tumors. Here we describe multiple small molecules capable of inhibiting RAC activation in acute lymphoblastic leukemia cell lines. One of these, DW0254, also demonstrates promising anti-leukemic activity in RAS-mutated cells. Using chemical proteomics and biophysical methods, we identified the hydrophobic pocket of phosphodiester 6 subunit delta (PDE6D), a known RAS chaperone, as a target for this compound. Inhibition of RAS localization to the plasma membrane upon DW0254 treatment is associated with RAC inhibition through a phosphatidylinositol-3-kinase/AKT-dependent mechanism. Our findings provide new insights into the importance of PDE6D-mediated transport for RAS-dependent RAC activation and leukemic cell survival.
Spot the match – wildlife photo-identification using information theory (2007)

The software and use of easily applied information-theoretic scores of match parsimony provide a reliable and freely available method for individual identification of wildlife, with wide applications and the potential to improve mark-recapture studies without resorting to invasive marking techniques.
Delivery of Hepatotrophic Factors Fails to Enhance Longer-Term Survival of Subcutaneously Transplanted Hepatocytes (2006)

Tissue engineering approaches have been investigated as a strategy for hepatocyte transplantation; however the death of a majority of transplanted cells critically limits success of these approaches. In a previous study, a transient increase in hepatocyte survival was achieved through delivery of vascular endothelial growth factor (VEGF) from the porous polymer scaffold utilized for cell delivery. To enhance longer-term survival of the hepatocytes, this delivery system was modified to additionally deliver epidermal growth factor (EGF) and hepatocyte growth factor (HGF) in a sustained manner. Hepatocytes were subcutaneously implanted in SCID mice on scaffolds containing EGF and/or HGF, in addition to VEGF, and survival was monitored for two weeks. A short-term enhancement of hepatocyte survival was observed after one week and is attributed to VEGF-enhanced vascularization, which was not altered by EGF or HGF. Surprisingly, long-term hepatocyte engraftment was not improved, as survival declined to the level of control conditions for all growth factor combinations after two weeks. This investigation indicates that the survival of hepatocytes transplanted into heterotopic locations is dependent on multiple signals. The delivery system developed for the current study may be useful in elucidating the specific factors controlling this process, and bring therapeutic transplantation of hepatocytes closer to implementation.
Ligand binding specificity of the <i>Escherichia coli</i> periplasmic histidine binding protein, HisJ (2016)

Abstract The HisJ protein from Escherichia coli and related Gram negative bacteria is the periplasmic component of a bacterial ATP‐cassette (ABC) transporter system. Together these proteins form a transmembrane complex that can take up L‐histidine from the environment and translocate it into the cytosol. We have studied the specificity of HisJ for binding L‐His and many related naturally occurring compounds. Our data confirm that L‐His is the preferred ligand, but that 1‐methyl‐L‐His and 3‐methyl‐L‐His can also bind, while the dipeptide carnosine binds weakly and D‐histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L‐Arg, homo‐L‐Arg, and post‐translationally modified methylated Arg‐analogs also bind with reasonable avidity, with the exception of symmetric dimethylated‐L‐Arg. In contrast, L‐Lys and L‐Orn have considerably weaker interactions with HisJ and methylated and acetylated Lys variants show relatively poor binding. It was also observed that the carboxylate group of these amino acids and their variants was very important for proper recognition of the ligand. Taken together our results are a key step towards designing HisJ as a specific protein‐based reagentless biosensor.
Design of a stand alone navigation system using position estimation algorithm (2009)

Applying low-cost sensors for the navigation of aircraft is an extremely challenging area. This paper presents an approach using dead reckoning by which aircrafts present position may be calculated from the knowledge of initial position and measurements of speed and acceleration. The main aim over here is to provide navigation information to the pilot on a cockpit display unit by using a standalone attitude and heading reference system and position estimation algorithm. This is helpful in navigation when GPS is non-operational or GPS drops out. The navigation loop provides continuous and reliable navigation solutions to the guidance and flight control loop for the flight. The whole navigation algorithm shall be implemented within an embedded display system that receives attitude information. This approach is also applicable for unmanned aerial vehicle and self-guided-rockets, where additional air-data and engine thrust data can be used for additional guidance and flight control.
Further total syntheses of chlorine-containing lichen xanthones (1980)

L. Fitzpatrick, T. Sala and M. V. Sargent, J. Chem. Soc., Perkin Trans. 1, 1980, 85 DOI: 10.1039/P19800000085
Distributed Ledger Technology and Blockchain (2017)

The financial sector is currently undergoing a major transformation, brought about by the rapid development and spread of new technologies. The confluence of ‘finance’ and ‘technology’ is often referred to as ‘Fintech’, typically describing companies or innovations that employ new technologies to improve or innovate financial services. ‘Fintech’ developments are seen across all areas of the financial sector, including payments and financial infrastructures, consumer and SMElending, insurance, investment management, and venture financing. This note on distributed ledger technology (DLT) and blockchains is part of a series of short notes that explore new trends and developments in Fintech and analyze their potential relevance for WBG activities. Forthcoming notes in this series will cover marketplace lending, ‘InsureTech’, and other topics. This note outlines the mechanisms, origins, and key characteristics of DLT; the difference between ‘public’ and ‘private’ DLT; the technology’s main advantages, challenges, and risks; relevant examples of DLT applications (with a focus on financial sector applications); and a brief overview of activities by governments, multilateral organization, and other stakeholders in this space. Finally, this note proposes next steps for the World Bank to study and evaluate areas where DLT could potentially be integrated into World Bank financial sector operations.
Control of the switching transients of IGBTs series strings by high-performance drive units (2003)

In the field of power electronics the use of series connected insulated gate devices, such as IGBTs or power MOSFETs, is interesting in order to obtain fast and efficient power switches in medium range power converters. In this kind of application, the control of the voltage sharing across the series strings of devices is an important aspect worth considering. The proposed technique allows safe commutations of the switches to be obtained by a simple and effective control circuit acting on the gate side of the power devices. In particular, the gate drive units are arranged in order to ensure good performances during the switching transients, while preventing overvoltage peaks on the devices. Both the design criteria and analysis of the control circuit are developed. Several experimental tests are reported in order to demonstrate the validity and correctness of the proposed approach.