gebhart/patrepeval huggingface dataset:
Supplementary Legends 1-2 from Loss of Keap1 Function Activates Nrf2 and Provides Advantages for Lung Cancer Cell Growth (2023)

Supplementary Legends 1-2 from Loss of Keap1 Function Activates Nrf2 and Provides Advantages for Lung Cancer Cell Growth
An analysis of the sponge Acanthostrongylophora igens' microbiome yields an actinomycete that produces the natural product manzamine A (2014)

Sponges have generated significant interest as a source of bioactive and elaborate secondary metabolites that hold promise for the development of novel therapeutics for the control of an array of human diseases. However, research and development of marine natural products can often be hampered by the difficulty associated with obtaining a stable and sustainable production source. Herein we report the first successful characterization and utilization of the microbiome of a marine invertebrate to identify a sustainable production source for an important natural product scaffold. Through molecular-microbial community analysis, optimization of fermentation conditions and MALDI-MS imaging, we provide the first report of a sponge-associated bacterium (<i>Micromonospora</i> sp.) that produces the manzamine class of antimalarials from the Indo-Pacific sponge <i>Acanthostrongylophora ingens</i> (Thiele, 1899) (Class Demospongiae, Order Haplosclerida, Family Petrosiidae). These findings suggest that a general strategy of analysis of the macroorganism's microbiome could significantly transform the field of natural products drug discovery by gaining access to not only novel drug leads, but the potential for sustainable production sources and biosynthetic genes at the same time.
Efficient Electron Injection Characteristics of Triazine Derivatives for Transparent OLEDs (TOLEDs) (2004)

Abstract We demonstrated that triazine (TRZ) derivatives possessing metal coordination sites in their structures showed excellent electron transport and injection characteristics in transparent organic light emitting diodes (TOLEDs). High luminescence efficiency with low driving voltage was observed with a TRZ/ITO cathode configuration (ITO: indium-tin-oxide), suggesting that the TRZ layer can efficiently accept electrons from the metal-oxide cathode layer, and inject electrons into an adjacent organic layer.
RNA replication by Q beta replicase: a working model. (1996)

Two classes of RNA ligands that bound to separate, high affinity nucleic acid binding sites on Q beta replicase were previously identified. RNA ligands to the two sites, referred to as site I and site II, were used to investigate the molecular mechanism of RNA replication employed by the four-subunit replicase. Replication inhibition by site I- and site II-specific ligands defined two subsets of replicatable RNAs. When provided with appropriate 3' ends, ligands to either site served as replication templates. UV crosslinking experiments revealed that site I is associated with the S1 subunit, site II with elongation factor Tu, and polymerization with the viral subunit of the holoenzyme. These results provide the framework for a three site model describing template recognition and product strand initiation by Q beta replicase.
Development of Planar Optics for an Optical Tracking Sensor (1998)

An optical tracking sensor for large-capacity flexible disk drive (FDD) is demonstrated. The passive optics is compact and lightweight (5.4 mm length×3.6 mm width×1.2 mm height in size and 18 mg weight). It comprises all passive optical elements necessary for optical tracking, e.g. , a focusing lens, a three-beam grating, an aperture and a beam splitter grating. Three beams were focused to a predetermined spot size of 13 µm at designed intervals of 110 µm on a disk surface and the reflected beams were successfully guided to photodiodes. This confirms that the application of the planar optical technique is very useful for realizing a compact and light optical sensor.
Three-dimensional simulations of electron beams focused by periodic permanent magnets (1999)

Summary form only given. A fully three-dimensional (3D) modal of an electron beam focused by a periodic permanent magnet (PPM) stack has been developed. First, the simulation code MAFIA was used to model a PPM stack using the magnetostatic solver. The exact geometry of the magnetic focusing structure was modeled; thus, no approximations were made regarding the off-axis fields. The fields from the static solver were loaded into the 3D particle-in-cell (PIC) solver of MAFIA where fully 3D behavior of the beam was simulated in the magnetic focusing field. Simulation results including beam current density, percent ripple and percent transmission will be presented, and the effects current, magnetic focusing strength and thermal velocities have on beam behavior will be demonstrated using 3D movies showing the evolution of beam characteristics in time and space. Unlike typical beam optics models, this 3D model allows simulation of asymmetric designs such as non-circularly symmetric electrostatic or magnetic focusing as well as the inclusion of input/output couplers.
Single-mode analysis of Yb-doped double-cladding distributed spectral filtering photonic crystal fibers (2010)

Hybrid large mode area Ytterbium-doped double-cladding photonic crystal fibers with anti-symmetric high refractive index inclusions provide efficient amplified spontaneous emission spectral filtering. Their performances have been analyzed by numerical simulations and experimental measurements. In particular, the fiber single-mode behaviour has been studied, by taking into account the fundamental and the first higher-order mode. Two approaches, the core down-doping and the reduction of the air-hole diameter in the inner cladding, have been successfully applied to reduce the higher-order mode content, regardless of the bending of the doped fiber, without significantly affecting its spectral filtering properties.
Scalable robotic-hand control system based on a hierarchical multi-processor architecture adopting a large number of tactile sensors (2012)

A robotic-hand controller with operating performance scalable according to the number of connected tactile sensors was developed. To eliminate performance bottlenecks that appear with increasing number of sensors, the controller architecture adopts multiple processors connected in a loosely-coupled hierarchical structure. Moreover, to maximize operation throughput of the system, a technique for gathering sensor data while all components operate asynchronously was also developed. A prototype robotic-hand system based on this architecture was constructed. The system experimentally demonstrated 62%-reduced control latency and 6.5-times faster sensor-data processing, thus achieving seven times greater performance scalability as compared with a conventional controller architecture. As a result, the proposed architecture enables the robotic-hand system to grasp objects with different weights and hardnesses.
Paper # 192: Therapeutic Advantage in Selective Ligament Augmentation for Partial Tears of Anterior Cruciate Ligament (2011)

BackgroundThe selected anterior cruciate ligament (ACL) augmentation procedure, either anteromedial (AM) or posterolateral (PL), has been introduced as a treatment of choice for the repair of partial ACL ruptures which is based on the double bundle anatomy of the ACL. The preserved mechanoreceptor and vascularity in the remnant ACL is thought to provide neurological and biological benefits. Although enhanced knee joint proprioception in ACL augmented patients has been previously reported, there are no studies that assess the biological healing advantages of the graft after the ACL augmentation procedure.
Human Hepatocyte Propagation System in the Mouse Livers: Functional Maintenance of the Production of Coagulation and Anticoagulation Factors (2012)

We previously reported that cell-based therapies using isolated hepatocytes including hepatocyte transplantation and liver tissue engineering approaches provide therapeutic benefits to hemophilia. For clinical application of these approaches, it is important to establish an active hepatocyte proliferation system that enables providing a sufficient number of hepatocytes. We also reported that human hepatocytes, which were transplanted into the liver of urokinase-type plasminogen activator transgenic severe combined immunodeficiency (uPA/SCID) mice, were able to proliferate while retaining their ability to produce coagulation factor IX. The objective of this study was to explore the functionalities of other coagulation and anticoagulation factors of the propagated human hepatocytes in uPA/SCID mice. Human hepatocytes were transplanted into the liver of uPA/SCID mice, and the propagation status of human hepatocytes in the mice was monitored by the increase in serum human albumin levels and immunohistochemical evaluation on the liver sections. Using uPA/SCID livers with various stages of human hepatocyte propagation, we analyzed the gene expression levels of coagulation factors (prothrombin, factor VII, factor X, and factor VIII) and anticoagulation factors (protein C and protein S) by real-time polymerase chain reaction (PCR) using human-specific primers. As a result, the total amount of raw messenger RNA expression levels increased in all genes analyzed according to the progress of hepatocyte propagation and proliferation. Except for factor VIII, the gene expression levels of the highly repopulated uPA/SCID mouse livers with human hepatocyte showed higher levels than those of normal human livers, indicating that propagated human hepatocytes in the uPA/SCID system possess full functions to produce most of the coagulation-related factors. The current work demonstrated that human hepatocytes can be propagated in experimental animals while maintaining normal gene expression levels of coagulation-related factors. It could be speculated that the propagated cells serve as a cell source for the treatment of various types of coagulation factor deficiencies.
A Method for Heat-Stimulated Compression of Poly(N-isopropyl acrylamide) Hydrogels Inside Single Giant Unilamellar Vesicles (2009)

In this letter, a hydrogel compression method for the facile generation of high polymer concentration within single giant unilamelar vesicles (GUV) is presented. A GUV with an internalized poly(N-isopropyl acrylamide) solution is heated above the lower critical solution temperature (LCST) until compartmentalization by collapsed hydrogel microaggregates occurs. Subsequently, the volume of the vesicle is decreased by reducing the area of the enclosing membrane. An increase in concentration by a factor of up to 11 is reached while the membrane remains intact, bringing the model system close to the living cell situation with its high concentration of proteins in the cytoplasm. The polymer-filled vesicles are also in a suitable density range to significantly improve the flow control performance of hydrogel valves embedded in soft matter nanofluidic devices.
CO2 capture performance of fluorinated porous carbon composite derived from a zinc-perfluoro metal-organic framework (2022)

Nanoporous carbon composite was derived via carbonization of a zinc-perfluoro metal organic framework {MOF: Zn-hfipbb (H2hfipbb = 4,4′-(hexafluoroisopropylidene)bis(benzoic acid))}. The MOF-derivative exhibits extra 0.5 nm and 5.5 nm pores in addition to 0.45 nm pores from bare Zn-hfipbb. Accordingly, BET surface areas (560–1000 m2 g−1) of Zn-hfipbb derived material greater than for Zn-hfipbb (360 m2 g−1) were obtained by varying carbonization temperatures in the range 500–900 °C, which trend is opposite those of other MOF derivative. The C-F bond of di-trifluoro on the aromatic ligand in an MOF structure is strong; therefore, some fluorine remains as C-F within the carbon structure after carbonization. The obtained MOF derived composite (carbonized at 700 °C) exhibits 5-times higher CO2 uptake than the pristine MOF does at 1000 kPa and 20 °C, and exhibits higher heat of adsorption for CO2 at zero-coverage. A breakthrough experiment using a CO2/N2 gas mixture (1:99 M ratio) demonstrated that Zn-hfippb derivative (carbonized at 700 °C) exhibits a longer breakthrough time and is repeatedly used as CO2 adsorbents under high humid condition.
Phospholipase D1 in Caveolae:  Regulation by Protein Kinase Cα and Caveolin-1 (1999)

Caveolae are small plasma membrane invaginations that have been implicated in cell signaling, and caveolin is a principal structural component of the caveolar membrane. Previously we have demonstrated that protein kinase Calpha (PKCalpha) directly interacts with phospholipase D1 (PLD1), activating the enzymatic activity of PLD1 in the presence of phorbol 12-myristate 13-acetate (PMA) [Lee, T. G., et al. (1997) Biochim. Biophys. Acta 1347, 199-204]. In this study, using a detergent-free procedure for the purification of a caveolin-enriched membrane fraction (CEM) and immunoblot analysis, we show that PLD1 is enriched in the CEMs of 3Y1 rat fibroblasts. Purified PLD1 directly bound to a glutathione S-transferase-caveolin-1 fusion protein in in vitro binding assays. The association of PLD1 with caveolin-1 could be completely eliminated by preincubation of PLD1 with an oligopeptide corresponding to the scaffolding domain (amino acids 82-101) of caveolin-1, indicating that caveolin-1 interacts with PLD1 through the scaffolding domain. The peptide also inhibited PKCalpha-stimulated PLD1 activity and the interaction between PLD1 and PKCalpha with an IC50 of 0.5 microM. PMA elicits translocation of PKCalpha to the CEMs, inducing PLD activation through the interaction of PKCalpha with PLD1 in the CEMs. Caveolin-1 also coimmunoprecipitated with PLD1 in the absence of PMA, and the amounts of coimmunoprecipitated caveolin-1 decreased in response to treatment with PMA. Taken together, our results suggest a new mechanism for the regulation of the PKCalpha-dependent PLD activity through the molecular interaction between PLD1, PKCalpha, and caveolin-1 in caveolae.
Synthesis of Deactoxycephalosporin C by a Mutant of Cephalosporium acremonium (1974)

A number of Cephalosporium acremonium mutants blocked in the synthesis of cephalosporin C were investigated for accumulation of other beta-lactam compounds. The non-cephalosporin C producers were isolated after exposing the superior cephalosporin C-producing strain M8650-4 to ultraviolet light (268 nm). One of the blocked mutants, MH63, accumulated deacetylcephalosporin C (0.4 mg/ml), deacetoxycephalosporin C (1.5 mg/ml), and penicillin N (2.7 mg/ml). In contrast, the parent of MH63 produced high levels of cephalosporin C as well as deacetylcephalosporin C (2.2 mg/ml) and penicillin N (1.0 mg/ml), but only traces of deacetoxycephalosporin C (about 0.1 mg/ml). Deacetoxycephalosporin C was isolated from the mutant strain and identified by ultraviolet light, nuclear magnetic resonance, bioactivity spectrum, and co-migration with authentic standard in three chromatography systems.
Decentralized minimum-cost repair for distributed storage systems (2013)

There have been emerging lots of applications for distributed storage systems e.g., those in wireless sensor networks or cloud storage. Since storage nodes in wireless sensor networks have limited battery, it is valuable to find a repair scheme with optimal transmission costs (e.g., energy). The optimal-cost repair has been recently investigated in a centralized way. However a centralized control mechanism may not be available or is very expensive. For the scenarios, it is interesting to study optimal-cost repair in a decentralized setup. We formulate the optimal-cost repair as convex optimization problems for the network with convex transmission costs. Then we use primal and dual decomposition approaches to decouple the problem into subproblems to be solved locally. Thus, each surviving node, collaborating with other nodes, can minimize its transmission cost such that the global cost is minimized. We further study the optimality and convergence of the algorithms. Finally, we discuss the code construction and determine the field size for finding feasible network codes in our approaches.
MedDRA Labeling Groupings to Improve Safety Communication in Product Labels (2022)

The granularity and structure of the International Council for Harmonisation's (ICH) Medical Dictionary for Regulatory Activities (MedDRA) are useful for precise coding of adverse events (AEs) for data analysis. In product labeling for healthcare practitioners, however, the granularity of MedDRA Preferred Terms (PTs) can obscure the communication of adverse reactions (ARs). Driven by a focus on patient safety, business needs, and regulatory guidance, many sponsors and regulators have begun to develop institution-specific approaches to clustering similar AR terms in medical product prescribing information on a product-by-product basis. However, there are no agreed upon conventions that describe which AR terms may be appropriate to group together. In order to improve safety communication to patients and healthcare providers, there is an urgent need for a harmonized international approach to the creation and use of groups of MedDRA PTs which we refer to as "MedDRA Labeling Groupings (MLGs)" in medical product prescribing information. Given its long-standing contributions towards the design of Standardised MedDRA Queries (SMQs), the Council for International Organizations of Medical Sciences (CIOMS) convened an Expert Working Group (EWG) with involvement of multiple major stakeholders to produce a consensus document on principles and points to consider in the development of MLGs. The CIOMS MLG EWG identified variations in grouping of MedDRA PTs in product labels, and in the current document, proposes a strategy for improving the communication of drug safety labeling. It is envisaged that the use of these consensus recommendations would be voluntary and applied to product labels in a manner that is consistent with existing regulatory frameworks.
When Polymer-based Acids can be used? A Core Flood Study (2009)

Abstract In-situ gelled acids that are based on polymers have been used in the field for several years, and were the subject of many lab studies. An extensive literature survey reveals that there are conflicting opinions about using these acids. On one hand, these acids were used in the field, with mixed results. Recent lab work indicated that these acids can cause damage under certain conditions. There is no agreement on when this system can be successfully applied in the field. A core flood study was conducted using Indiana limestone cores (1.5 in. diameter &amp; 20 in. long) at high temperatures and pressures. Propagation of the acid, polymer, and cross-linker inside the long cores was examined for the first time in detail. Samples of the core effluent were collected and the concentrations of calcium, cross-linker, and acid were measured. Permeability enhancement and location of any precipitation was detected using CT scanner to the core after, and before the acid injection. Different sections were cut from the core to investigate the propagation, and precipitation of polymer and cross-linker. Material balance was conducted to determine the amounts of cross-liker that retained in the core. Experimental results show that this acid system caused damage in some cases. At low shear rates, in-situ gelled acid formed a gel inside the core, as indicated by the cyclic behavior noted in the pressure drop across the core, and the acid changed direction inside the core several times. However, this gel significantly reduced the core permeability. At high shear rates, a smaller amount of gel was formed inside the core and the acid did change its direction inside the core. A significant permeability enhancement was achieved. Wormhole length increased as the shear rate was increased, while the diameter of wormhole increased as the cumulative injected volume of acid was increased. CT scan indicated the presence of gel residue inside the and around the worm hole. Gel residue increased at low shear rates. Material balance on the cross-linker indicated that a significant amount of the cross-linker was retained in the core. This amount increased at low shear rates.
A Low-Cost PC Controlled System for Measurement of Vector Reflection Coefficient in ISM Band (2006)

This paper describes design of a prototype of a very low-cost ISM band reflectometer for measurement of a vector reflection coefficient. The device is based on integrated circuit AD8302 by Analog Devices. Switched phase shifter is used to resolve the problem of ambiguity of the sign of the phase shift. The system is controlled by a dedicated digital circuit and PC user interface. The system was designed for the band 2.3 GHz to 2.6 GHz as an inexpensive measurement alternative in manufacturing and maintenance of heating and telecommunication systems in that band. The paper provides accuracy analysis indicating the accuracy levels which can be expected from devices of that class.
Quantifying Disrupted Outer Retinal-Subretinal Layer in SD-OCT Images in Choroidal Neovascularization (2014)

Purpose.: We reported a fully automated method to identify and quantify the thickness of the outer retinal-subretinal (ORSR) layer from clinical spectral-domain optical coherence tomography (SD-OCT) scans of choroidal neovascularization (CNV) due to exudative age-related macular degeneration (eAMD). Methods.: A total of 23 subjects with CNV met eligibility. Volumetric SD-OCT scans of 23 eyes were obtained (Zeiss Cirrus, 200 × 200 × 1024 voxels). In a subset of eyes, scans were repeated. The OCT volumes were analyzed using our standard parameters and using a 3-dimensional (3D) graph-search approach with an adaptive cost function. A retinal specialist graded the segmentation as generally accurate, local segmentation inaccuracies, or failure. Reproducibility on repeat scans was analyzed using root mean square coefficient of variation (RMS CV) of the average ORSR thickness. Results.: Using a standard segmentation approach, 1/23 OCT segmentations was graded generally accurate and 22/23 were failure(s). With the adaptive method 21/23 segmentations were graded generally accurate; 2/23 were local segmentation inaccuracies and none was a failure. The intermethod quality of segmentation was significantly different (P << 0.001). The average ORSR thickness measured on CNV patients (78.0 μm; 95% confidence interval [CI], 72.5–83.4 μm) is significantly larger (P << 0.001) than normal average ORSR layer thickness (51.5 ± 3.3 μm). The RMS CV was 8.1%. Conclusions.: We have developed a fully automated 3D method for segmenting the ORSR layer in SD-OCT of patients with CNV from eAMD. Our method can quantify the ORSR layer thickness in the presence of fluid, which has the potential to augment management accuracy and efficiency of anti-VEGF treatment.