gebhart/patrepeval huggingface dataset:
Abstract A62: Phosphorylation of Ser205 by the protein kinase CK2 persists on Pax3-FOXO1, but not Pax3, throughout myogenic differentiation (2009)

Abstract The myogenic transcription factor Pax3 plays an essential role in early skeletal muscle development and is a key component in Alveolar rhabdomyosarcoma (ARMS), a childhood solid muscle tumor. ARMS, which is associated with a four year survival rate of only 17%, is most commonly characterized by a t(2;13) chromosomal translocation resulting in the fusion of the 5′ Pax3 sequences to the 3′ FOXO1 sequences to encode the oncogenic fusion protein, Pax3-FOXO1. Posttranslational modifications such as phosphorylation are common mechanisms by which transcription factors are regulated. Consistent with this fact, we demonstrated in a previous report that Pax3 is phosphorylated on Ser205 in proliferating, but not differentiated, primary myoblasts. However, the kinase that mediates this phosphorylation event has yet to be identified. More recently it was demonstrated that Pax3-FOXO1 is also phosphorylated at unidentified sites in non-physiologically relevant cells. Despite this information, it is not known whether Pax3-FOXO1 is phosphorylated at Ser205 or how the phosphorylation of the fusion protein changes during myogenic differentiation. In this report, we use standard in vitro kinase assays to identify CK2 (formerly termed “casein kinase II”) as the kinase responsible for phosphorylating Pax3 and Pax3-FOXO1 at Ser205 in proliferating mouse primary myoblasts. Furthermore, we use standard Western blot analysis to demonstrate that in contrast to wild-type Pax3, phosphorylation at Ser205 persists on Pax3-throughout early myogenic differentiation. Finally, we use standard Western blot analysis to show that Pax3-FOXO1 is phosphorylated at Ser205 in a variety of translocation-containing ARMS cell lines. The results presented in this report not only suggest a possible mechanism by which the disregulation of Pax3-FOXO1 may contribute to tumorigenesis, but also identifies a novel target for the development of therapies to be used for the treatment of ARMS. Citation Information: Cancer Res 2009;69(23 Suppl):A62.
Air-bubble-triggered drop formation in microfluidics (2011)

In microfluidic devices, droplets are normally formed using T-junction or flow focus mechanisms. While both afford a high degree of control over drop formation, they are limited in maximum production rate by the jetting transition. Here, we introduce a new drop formation mechanism that is not limited by jetting, allowing much faster drop production.
ROS-mediated carbon monoxide and drug release from drug-conjugated carboxyboranes (2017)

Elevated levels of reactive oxygen species (ROS) are associated with several detrimental diseases. Therefore, using this condition for selective treatments could be a great advantage in fighting these disorders. Here, we present amine carboxyboranes as a class of molecules for therapeutic CO gas generation and for delivering drug molecules in the presence of ROS. Our findings indicate amine carboxyboranes to be very slow CO releasers at physiological pH and temperature without any inducers but generate CO faster when reacted with a non-radical ROS (H<sub>2</sub>O<sub>2</sub>). Furthermore, a radical ROS (˙OH) dramatically expedites the production of CO from amine carboxyboranes. A decomposition profile shows the release of the amine group during the decarbonylation process from drug-conjugated carboxyboranes. This suggests that the carboxyborane moiety can be a useful tool for the delivery of amine-containing drugs to disease sites which display abundant ROS levels.
Krüppel-like Factor 7 engineered for transcriptional activation promotes axon regeneration in the adult corticospinal tract (2012)

Axon regeneration in the central nervous system normally fails, in part because of a developmental decline in the intrinsic ability of CNS projection neurons to extend axons. Members of the KLF family of transcription factors regulate regenerative potential in developing CNS neurons. Expression of one family member, KLF7, is down-regulated developmentally, and overexpression of KLF7 in cortical neurons in vitro promotes axonal growth. To circumvent difficulties in achieving high neuronal expression of exogenous KLF7, we created a chimera with the VP16 transactivation domain, which displayed enhanced neuronal expression compared with the native protein while maintaining transcriptional activation and growth promotion in vitro. Overexpression of VP16-KLF7 overcame the developmental loss of regenerative ability in cortical slice cultures. Adult corticospinal tract (CST) neurons failed to up-regulate KLF7 in response to axon injury, and overexpression of VP16-KLF7 in vivo promoted both sprouting and regenerative axon growth in the CST of adult mice. These findings identify a unique means of promoting CST axon regeneration in vivo by reengineering a developmentally down-regulated, growth-promoting transcription factor.
Document filtering method using non-relevant information profile (2000)

Document filtering is a task to retrieve documents relevant to a user's profile from a flow of documents. Generally, filtering systems calculate the similarity between the profile and each incoming document, and retrieve documents with similarity higher than a threshold. However, many systems set a relatively high threshold to reduce retrieval of non-relevant documents, which results in the ignorance of many relevant documents. In this paper, we propose the use of a non-relevant information profile to reduce the mistaken retrieval of non-relevant documents. Results from experiments show that this filter has successfully rejected a sufficient number of non-relevant documents, resulting in an improvement of filtering performance.
The Design of High-Performance Dynamic Asynchronous Pipelines: High-Capacity Style (2007)

This paper introduces a high-throughput asynchronous pipeline style, called high-capacity (HC) pipelines, targeted to datapaths that use dynamic logic. This approach includes a novel highly-concurrent handshake protocol, with fewer synchronization points between neighboring pipeline stages than almost all existing asynchronous dynamic pipelining approaches. Furthermore, the dynamic pipelines provide 100% buffering capacity, without explicit latches, by means of separate pullup and pulldown control for each pipeline stage: neighboring stages can store distinct data items, unlike almost all existing latchless dynamic asynchronous pipelines. As a result, very high throughput is obtained. Fabricated first-input-first-output (FIFO) designs, in 0.18-m technology, were fully functional over a wide range of supply voltages (1.2 to over 2.5 V), exhibiting a corresponding range of throughputs from 1.0-2.4 giga items/s. In addition, an experimental finite-impulse response (FIR) filter chip was designed and fabricated with IBM Research, whose speed-critical core used an HC pipeline. The HC pipeline exhibited throughputs up to 1.8 giga items/s, and the overall filter achieved 1.32 giga items/s, thus obtaining 15% higher throughput and 50% lower latency than the fastest previously-reported synchronous FIR filter, also designed at IBM Research.
Oxygen Saturation Measurements of Blood in Retinal Vessels during Blood Loss (1998)

We describe a noninvasive technique and instrumentation for measuring the oxygen saturation of blood in retinal arteries and veins. The measurements are made by shining low-power lasers into the eye, and scanning the beams across a retinal blood vessel. The light reflected and scattered back out of the eye is collected and measured. The oxygen saturation of blood within the vessel is determined by analyzing the vessel absorption profiles at two wavelengths. A complete saturation measurement can be made in less than 1 s, allowing real-time measurement during physiologic changes. The sensitivity of this measurement technique to changes in retinal saturation has been demonstrated through a series of pilot studies in anesthetized swine. We present data indicating that retinal venous oxygen saturation decreases during ongoing blood loss, demonstrating a potential application of an eye oximeter to noninvasively monitor blood loss. © 1998 Society of Photo-Optical Instrumentation Engineers.
Enhanced Quantification of Retinal Perfusion by Improved Discrimination of Blood Flow From Bulk Motion Signal in OCTA (2018)

The rb-BMS method helped reduce the inter-scan variability by generating accurate vessel maps, improving the reliability of retinal perfusion quantification.
Recent advances for spermatogonial stem cell transplantation in livestock (2017)

At the foundation of spermatogenesis are the actions of spermatogonial stem cells (SSCs), and a remarkable feature of these cells is the capacity to regenerate spermatogenesis following transplantation into testes of a recipient male that lacks endogenous germline. This ability could be exploited in livestock production as a breeding tool to enhance genetic gain. A key element to success is derivation of culture conditions that support proliferation of SSCs to provide sufficient numbers of cells for transfer into multiple recipient males. Using methodology devised for rodent cells as a foundation, advances in culturing cattle SSCs have occurred over the past few years and efforts are underway to extend this capability to pig cells. Another critical component to SSC transplantation is generation of males with germline ablation but intact somatic support cell function that can serve as surrogate sires for donor-derived spermatogenesis in a natural mating scheme. Recent advances in pigs using gene editing technologies have demonstrated that knockout of a key male germ cell-specific gene, namely NANOS2, leads to male-specific germline ablation but otherwise normal physiology, including intact seminiferous tubules. Together with recent advances in culturing spermatogonia of higher-order mammals, the now efficient means of producing germline-ablated recipient males have brought the application of SSC transplantation in livestock as a production tool closer to reality than ever before.
Synthesis and Structure of the Bidimensional Zeolite ITQ-32 with Small and Large Pores (2005)

A new bidimensional zeolite containing 8R and 12R pores, denoted as ITQ-32, has been synthesized and its structure solved from powder X-ray diffraction data. This zeolite presents a relatively large pore volume (0.16 cm3/g) and pore apertures of 3.5 x 4.3 A and can be prepared as a nearly pure silica zeolite and as aluminosilicate. In the latest case, acidic properties are developed.
Inhibition of <i>Clostridium histolyticum</i> collagenases by phosphonamide peptide inhibitors (1990)

Several phosphonamide peptides having the general structure R‐PO(OH)‐Xaa‐Yaa‐Zaa were synthesized and tested for inhibition of Clostridium histolyticum collagenase. Inhibition was found to depend on the nature of R, Xaa, Yaa and Zaa such that the maximal affinity ( K i = 5 nM) was observed when R = p ‐nitrophenylethyl, Xaa = Gly, Yaa = Pro and Zaa = 2‐aminohexanoic acid; this represents the tightest binding of inhibitor reported to date for any bacterial collagenase. Substitution of the p ‐nitrophenylethyl by a methyl group led to a 500‐fold decrease of the potency, highlighting the existence of optimal interaction between the nitrophenylethyl side chain and one subsite of the enzyme. Replacement of the NH group in glycine residue (Xaa position) by ‐O‐ or ‐N‐CH 3 produces significantly less potent inhibitors, presumably due in part to the loss of a hydrogen bond between the inhibitor and collagenase active site. These phosphonamidates are thought to be acting as transition‐state analogues of the peptide substrate.
A tunable Marchand balun at K band in silicon germanium (SiGe) technology (2015)

This paper presents the design of a switch-based, tunable Marchand balun at K band. The tunability is achieved by using pass gate CMOS structures that ideally switch in or out sections of the balun, thereby controlling its frequency response. The balun is fabricated in a high performance SiGe BiCMOS process with standard 180 nm CMOS technology. The ability to tune the response across a frequency range is demonstrated. The balun is characterized in terms of mixed signal scattering parameters. Extensive layout and simulations have been executed. The authors believe this is the first demonstration of a tunable balun using pass gate structures to change the lengths of the balun windings in the high region of the microwave range.
High-Density Recording Using Phase-Change Optical Disk (1994)

High-track-density recording has been investigated using a phase-change optical disk. Crosstalk was measured as a function of track pitch. Crosstalk of less than -26 dB was obtained at the track pitch of 1.0 µm using a red laser diode, an objective lens of large numerical aperture and a thin substrate. Amorphous marks were observed by transmission electron microscopy, and it was found that the width of amorphous marks remains on the order of the groove width even at high recording power, though the length increases with the increase of the recording power.
A Co-processor for Computing the Euler Number of a Binary Image using Divide-and-Conquer Strategy (2007)

Euler number is a fundamental topological feature of an image. The efficiency of computation of topological features of an image is critical for many digital imaging applications such as image matching, database retrieval, and computer vision that require real time response. In this paper, a novel algorithm for computing the Euler number of a binary image based on divide-andconquer paradigm, is proposed, which outperforms significantly the conventional techniques used in image processing tools. The algorithm can be easily parallelized for computing the Euler number of an N × N image in O(N) time, with O(N) processors. Using a simple architecture, the proposed method can be implemented as a special purpose VLSI chip to be used as a co-processor.
Facile Removal of Homogeneous SABRE Catalysts for Purifying Hyperpolarized Metronidazole, a Potential Hypoxia Sensor (2018)

We report a simple and effective method to remove IrIMes homogeneous polarization transfer catalysts from solutions where NMR Signal Amplification By Reversible Exchange (SABRE) has been performed, while leaving intact the substrate's hyperpolarized state. Following microTesla SABRE hyperpolarization of <sup>15</sup>N spins in metronidazole, addition of SiO<sub>2</sub> microparticles functionalized with 3-mercaptopropyl or 2-mercaptoethyl ethyl sulfide moieties provides removal of the catalyst from solution well within the hyperpolarization decay time at 0.3 T (<i>T</i> <sub>1</sub>>3 mins)-and enabling transfer to 9.4 T for detection of enhanced <sup>15</sup>N signals in the absence of catalyst within the NMR-detection region. Successful catalyst removal from solution is supported by the inability to "re-hyperpolarize" <sup>15</sup>N spins in subsequent attempts, as well as by <sup>1</sup>H NMR and ICP-MS. Record-high <sup>15</sup>N nuclear polarization of up to ~34% was achieved, corresponding to >100,000-fold enhancement at 9.4 T, and approximately 5/6<sup>th</sup> of the <sup>15</sup>N hyperpolarization is retained after ~20-second-long purification procedure. Taken together, these results help pave the way for future studies involving <i>in vivo</i> molecular imaging using agents hyperpolarized via rapid and inexpensive parahydrogen-based methods.
Transport Phenomena in Two-Phase Micro-Channel Heat Sinks (2004)

The design and reliable operation of a two-phase micro-channel heat sink require a fundamental understanding of the complex transport phenomena associated with convective boiling in small, parallel coolant passages. This understanding is the primary goal of this paper. This goal is realized by exploring the following aspects of boiling in micro-channels: hydrodynamic instability, two-phase flow patterns, pressure drop, and convective boiling heat transfer. High-speed photographic methods were used to determine dominant flow patterns and explore as well as characterize hydrodynamic instabilities. Two types of dynamic instability were identified, a severe pressure drop oscillation and a mild parallel channel instability, and a simple method is recommended to completely suppress the former. Predictions of three popular two-phase pressure drop models and correlations were compared to micro-channel water data, and only a separated flow (Lockhart-Martinelli) correlation based on the assumption of laminar flow in both phases gave acceptable predictions. Several popular heat transfer correlations were also examined and deemed unsuitable for micro-channel heat sinks because all these correlations are based on turbulent flow assumptions, and do not capture the unique features of micro-channel flow such as abrupt transition to slug flow, hydrodynamic instability, and high droplet entrainment in the annular regime. These findings point to the need for further study of boiling behavior and new predictive tools specifically tailored to micro-channel heat sinks.
Synthesis of high-quality CdSe nanocrystals in heat transfer fluids (2005)

Fluorescent semiconductor nanoparticles, or quantum dots, have potential uses as an optical material, in which the optoelectronic properties can be tuned precisely by particle size. Advances in chemical synthesis have led to improvements in size and shape control, cost, and safety. A limiting step in large-scale production is identified to be the raw materials cost, in which a common synthesis solvent, octadecene, accounts for most of the materials cost in a batch of CdSe quantum dots. Thus, less expensive solvents are needed. In this paper, we identify heat transfer fluids, a class of organic liquids commonly used in chemical process industries to transport heat between unit operations, as alternative solvents for quantum dot synthesis. We specifically show that two heat transfer fluids can be used successfully in the synthesis of CdSe quantum dots with uniform particle sizes. We observe differences in particle growth using the various solvents.
Anti-tumor efficacy study of the Bruton’s tyrosine kinase (BTK) inhibitor, ONO/GS-4059, in combination with the glycoengineered type II anti-CD20 monoclonal antibody obinutuzumab (GA101) demonstrates superior<i>in vivo</i>efficacy compared to ONO/GS-4059 in combination with rituximab (2016)

The activated B-cell diffuse large B-cell-like lymphoma (ABC-DLBCL) correlates with poor prognosis. The B-cell receptor signaling pathway is known to be dysregulated in NHL/CLL and given BTK is a downstream mediator of BCR signaling, BTK constitutes an interesting and obvious therapeutic target. Given the high potency and selectivity of the BTK inhibitor, ONO/GS-4059, it was hypothesized that, the anti-tumor activity of ONO/GS-4059 could be further enhanced by combining it with the anti-CD20 Abs, rituximab (RTX) or obinutuzumab (GA101). ONO/GS-4059 combined with GA101 or RTX was significantly better than the respective monotherapy with tumor growth inhibition (TGI) of 90% for the GA101 combination and 86% for the RTX combination. In contrast, ibrutinib (PCI-32765) combined with RTX did not result in improved efficacy compared with respective monotherapy. Taken together these data indicate that the combination of ONO/GS-4059 with rituximab and particularly obinutuzumab may be an effective treatment for ABC-DLBCL.
A novel parallel architecture for a switched-capacitor bandpass sigma-delta modulator (2002)

In this paper, we apply parallelism by 4/spl times/ of analog signal processors to the design of a bandpass sigma-delta modulator. We show that the overall speed of the modulator is increased without increasing the speed requirement of the individual building blocks. Several architectures are considered in terms of their resilience to implementation details such as mismatch and gain errors. A switched capacitor circuit is also presented for the proposed modulator.
Self‐calibrating GRAPPA operator gridding for radial and spiral trajectories (2008)

Self-calibrating GRAPPA operator gridding (GROG) is a method by which non-Cartesian MRI data can be gridded using spatial information from a multichannel coil array without the need for an additional calibration dataset. Using self-calibrating GROG, the non-Cartesian datapoints are shifted to nearby k-space locations using parallel imaging weight sets determined from the datapoints themselves. GROG employs the GRAPPA Operator, a special formulation of the general reconstruction method GRAPPA, to perform these shifts. Although GROG can be used to grid undersampled datasets, it is important to note that this method uses parallel imaging only for gridding, and not to reconstruct artifact-free images from undersampled data. The innovation introduced here, namely, self-calibrating GROG, allows the shift operators to be calculated directly out of the non-Cartesian data themselves. This eliminates the need for an additional calibration dataset, which reduces the imaging time and also makes the GROG reconstruction more robust by removing possible inconsistencies between the calibration and non-Cartesian datasets. Simulated and in vivo examples of radial and spiral datasets gridded using self-calibrating GROG are compared to images gridded using the standard method of convolution gridding.
Reinforcement of Shear Thinning Protein Hydrogels by Responsive Block Copolymer Self‐Assembly (2012)

Shear thinning hydrogels are promising materials that exhibit rapid self-healing following the cessation of shear, making them attractive for a variety of applications including injectable biomaterials. In this work, self-assembly is demonstrated as a strategy to introduce a reinforcing network within shear thinning artificially engineered protein gels, enabling a responsive transition from an injectable state at low temperatures with a low yield stress to a stiffened state at physiological temperatures with resistance to shear thinning, higher toughness, and reduced erosion rates and creep compliance. Protein-polymer triblock copolymers capable of the responsive self-assembly of two orthogonal networks have been synthesized by conjugating poly(N-isopropylacrylamide) to the N- and C- termini of a protein midblock decorated with coiled-coil self-associating domains. Midblock association forms a shear-thinning network, while endblock aggregation at elevated temperatures introduces a second, independent physical network into the protein hydrogel. These new, reversible crosslinks introduce extremely long relaxation times and lead to a five-fold increase in the elastic modulus, significantly larger than is expected from transient network theory. Thermoresponsive reinforcement reduces the high temperature creep compliance by over four orders of magnitude, decreases the erosion rate by at least a factor of five, and increases the yield stress by up to a factor of seven. The reinforced hydrogels also exhibit enhanced resistance to plastic deformation and failure in uniaxial compression. Combined with the demonstrated potential of shear thinning artificial protein hydrogels for various uses, including the minimally-invasive implantation of bioactive scaffolds, this reinforcement mechanism broadens the range of applications that can be addressed with shear-thinning physical gels.
Altered Functionality of Anti-Bacterial Antibodies in Patients with Chronic Hepatitis C Virus Infection (2013)

Anti-gal antibodies in patients with liver cirrhosis were reduced in their ability to mediate complement mediated lysis of target cells. As bacterial infection is a major complication in patients with cirrhosis and bacterial products such as LPS are thought to play a major role in the development and progression of liver fibrosis, this finding has many clinical implications in the etiology, prognosis and treatment of liver disease.