gebhart/patrepeval huggingface dataset:
Preparation of capped RNA transcripts using T7 RNA polymerase (1986)

Journal Article Preparation of capped RNA transcripts using T7 RNA polymerase Get access David A. Nielsen, David A. Nielsen Department of Biochemistry, University of Illinois1209 West California Street, Urbana, IL 61801, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar David J. Shapiro David J. Shapiro Department of Biochemistry, University of Illinois1209 West California Street, Urbana, IL 61801, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 14, Issue 14, 11 July 1986, Page 5936, https://doi.org/10.1093/nar/14.14.5936 Published: 11 July 1986 Article history Received: 12 June 1986 Published: 11 July 1986
Determinants of Cytochrome c Pro-apoptotic Activity (2000)

Cytochrome c released from vertebrate mitochondria engages apoptosis by triggering caspase activation. We previously reported that, whereas cytochromes c from higher eukaryotes can activate caspases in Xenopus egg and mammalian cytosols, iso-1 and iso-2 cytochromes c from the yeast Saccharomyces cerevisiae cannot. Here we examine whether the inactivity of the yeast isoforms is related to a post-translational modification of lysine 72, N-epsilon-trimethylation. This modification was found to abrogate pro-apoptotic activity of metazoan cytochrome c expressed in yeast. However, iso-1 cytochrome c lacking the trimethylation modification also was devoid of pro-apoptotic activity. Thus, both lysine 72 trimethylation and other features of the iso-1 sequence preclude pro-apoptotic activity. Competition studies suggest that the lack of pro-apoptotic activity was associated with a low affinity for Apaf-1. As cytochromes c that lack apoptotic function still support respiration, different mechanisms appear to be involved in the two activities.
Transforming growth factor-beta 1 modulates basic fibroblast growth factor-induced proteolytic and angiogenic properties of endothelial cells in vitro. (1990)

Tightly controlled proteolytic degradation of the extracellular matrix by invading microvascular endothelial cells is believed to be a necessary component of the angiogenic process. We have previously demonstrated the induction of plasminogen activators (PAs) in bovine microvascular endothelial (BME) cells by three agents that induce angiogenesis in vitro: basic FGF (bFGF), PMA, and sodium orthovanadate. Surprisingly, we find that these agents also induce plasminogen activator inhibitor-1 (PAI-1) activity and mRNA in BME cells. We also find that transforming growth factor-beta 1 (TGF-beta 1), which in vitro modulates a number of endothelial cell functions relevant to angiogenesis, also increases both PAI-1 and urokinase-type PA (u-PA) mRNA. Thus, production of both proteases and protease inhibitors is increased by angiogenic agents and TGF-beta 1. However, the kinetics and amplitude of PAI-1 and u-PA mRNA induction by these agents are strikingly different. We have used the ratio of u-PA:PAI-1 mRNA levels as an indicator of proteolytic balance. This ratio is tilted towards enhanced proteolysis in response to bFGF, towards antiproteolysis in response to TGF-beta 1, and is similar to that in untreated cultures when the two agents are added simultaneously. Using an in vitro angiogenesis assay in three-dimensional fibrin gels, we find that TGF-beta 1 inhibits the bFGF-induced formation of tube-like structures, resulting in the formation of solid endothelial cell cords within the superficial parts of the gel. These results suggest that a net positive proteolytic balance is required for capillary lumen formation. A novel perspective is provided on the relationship between extracellular matrix invasion, lumen formation, and net proteolytic balance, thereby reflecting the interplay between angiogenesis-modulating cytokines such as bFGF and TGF-beta 1.
Detection of complement activation using monoclonal antibodies against C3d (2013)

During complement activation the C3 protein is cleaved, and C3 activation fragments are covalently fixed to tissues. Tissue-bound C3 fragments are a durable biomarker of tissue inflammation, and these fragments have been exploited as addressable binding ligands for targeted therapeutics and diagnostic agents. We have generated cross-reactive murine monoclonal antibodies against human and mouse C3d, the final C3 degradation fragment generated during complement activation. We developed 3 monoclonal antibodies (3d8b, 3d9a, and 3d29) that preferentially bind to the iC3b, C3dg, and C3d fragments in solution, but do not bind to intact C3 or C3b. The same 3 clones also bind to tissue-bound C3 activation fragments when injected systemically. Using mouse models of renal and ocular disease, we confirmed that, following systemic injection, the antibodies accumulated at sites of C3 fragment deposition within the glomerulus, the renal tubulointerstitium, and the posterior pole of the eye. To detect antibodies bound within the eye, we used optical imaging and observed accumulation of the antibodies within retinal lesions in a model of choroidal neovascularization (CNV). Our results demonstrate that imaging methods that use these antibodies may provide a sensitive means of detecting and monitoring complement activation-associated tissue inflammation.
Update on 2-D array transducers for medical ultrasound (2002)

l 1/2 -D and 2-D arrays offer a myriad of new imaging modalities and benefits when compared to the linear array. However, with added benefits come many problems and challenges and l 1/2 -D and 2-D arrays are no exception. The authors give possible solutions to a number of these challenges. The increase in transducer channels needed in a 1 1/2 -D and 2-D array can be reduced using a sparse periodic or sparse random array. The complexity of the fabrication is overcome using a multilayer flexible connector designed and fabricated using microelectronic techniques. The low SNR of 1 1/2 -D and 2-D arrays can be circumvented with the application of multi-layer ceramic elements to optimize the SNR given a specific transmit and receive configuration. In addition, optoelectronic transmitters allow for the reduction in size and increase in flexibility of the transducer cable because of the use of fiber optics. With the reduction in the number of channels, improvement in transducer fabrication, and increase in transducer SNR, l 1/2 -D and 2-D arrays will be accepted as viable replacements for the linear arrays of today.
Manufacturable mobile phone optics: higher order aspheres are not always better (2010)

We provide an overview of the design drivers for mobile camera phone cameras, with particular attention paid to aspheric order. The designer is often tempted to use high order aspheres (e.g. 18th order). However, better as-built performance can often be obtained at lower orders.
DL-Learner Manual (2015)

1 What is DL-Learner? 2 2 Getting Started 3 3 DL-Learner Architecture 4 4 DL-Learner Components 5 4.1 Knowledge Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 4.2 Reasoner Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 4.3 Learning Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 4.4 Learning Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 5 DL-Learner Interfaces 10 6 Extending DL-Learner 11 7 General Information 13
Simulated Car Crashes at Intersections in Drivers With Alzheimer Disease (2001)

Current evidence suggests that car crashes in cognitively impaired older drivers often occur because of failure to notice other drivers at intersections. We tested whether licensed drivers with mild to moderate cognitive impairment due to Alzheimer disease (AD) are at greater risk for intersection crashes. In this experiment, 30 participants drove on a virtual highway in a simulator scenario where the approach to within 3.6 seconds of an intersection triggered an illegal incursion by another vehicle. To avoid collision with the incurring vehicle, the driver had to perceive, attend to, and interpret the roadway situation; formulate an evasive plan; and then exert appropriate action on the accelerator, brake, or steering controls, all under pressure of time. The results showed that 6 of 18 drivers with AD (33%) experienced crashes versus none of 12 nondemented drivers of similar age. Use of a visual tool that plots control over steering wheel position, brake and accelerator pedals, vehicle speed, and vehicle position during the 5 seconds preceding a crash event showed inattention and control responses that were either inappropriate or too slow. The findings were combined with those in another recent study of collision avoidance in drivers with AD that focused on potential rear end collisions. Predictors of crashes in the combined studies included visuospatial impairment, disordered attention, reduced processing of visual motion cues, and overall cognitive decline. The results help to specify the linkage between decline in certain cognitive domains and increased crash risk in AD and also support the use of high-fidelity simulation and neuropsychologic assessment in an effort to standardize the assessment of fitness to drive in persons with medical impairments.
A Fully ZVS Critical Conduction Mode Boost PFC (2011)

Boost converter operating in critical conduction mode is widely used in low-power power factor corrector because of its simplicity and low switching losses. The switching loss due to parasitic capacitor discharge at the on-time instant can also be reduced by a valley switching technique. In this paper, we introduce a new driver topology for the high-side switch in a synchronous boost converter operating in the critical conduction mode to obtain full zero-voltage switching. Using the proposed high-side driver topology, the conventional control circuit is sufficient to control the low-side switch, and no additional control circuit is required to adjust the timing of the switches. Finally, the line current distortion is reduced through the use of on-time extension technique to less than 10% in the defined load range. Based on approximate mathematical calculations, two separate distortion reduction circuits are designed to implement the on-time extension technique for both voltage-mode and current-mode control methods.
A potent inhibitor of normal and transformed cell growth derived from contact-inhibited cells. (1978)

Abstract Contact inhibition of growth (density-dependent regulation) is a form of in vitro growth control, the loss of which is correlated with in vivo tumorigenicity. A diffusible factor prepared from culture medium of a contact-inhibited line of hamster melanocytes has previously been found to restore the capacity for contact inhibition of growth to malignant melanocytes of man, mouse, and hamster, while also producing characteristic morphological changes. In the present studies the species specificity of the growth inhibitory effect was examined. The melanocyte contact inhibitory factor (MCIF) was found to inhibit growth in vitro of a broad spectrum of malignant cell types of ectodermal, mesodermal, and endodermal origin. Inhibition characterized by decreased saturation densities of cultures, growth in monolayers, and individual cell enlargement was dose dependent, reversible, and nontoxic at concentrations of 100 to 200 µg/ml), MCIF was selectively lethal to malignant, non-contact-inhibited (compared to benign, contact-inhibited) cell types. A fraction analogous to MCIF, prepared from culture medium of a line of contact-inhibited human epidermal cells and containing a protein electrophoretically identical with the major protein present in MCIF (M.W. about 160,000), was functionally identical with MCIF in both morphological and growth inhibitory effects on malignant melanocytes. The growth regulatory macromolecular component(s) produced by contact-inhibited cells is able to restore some aspects of cell surface-mediated in vitro growth control to malignant cells. Such components may eventually provide a new class of cell surface-active agents for control of neoplastic growth.
Communication via gap junctions underlies early functional and beneficial interactions between grafted neural stem cells and the host (2010)

How grafted neural stem cells (NSCs) and their progeny integrate into recipient brain tissue and functionally interact with host cells is as yet unanswered. We report that, in organotypic slice cultures analyzed by ratiometric time-lapse calcium imaging, current-clamp recordings, and dye-coupling methods, an early and essential way in which grafted murine or human NSCs integrate functionally into host neural circuitry and affect host cells is via gap-junctional coupling, even before electrophysiologically mature neuronal differentiation. The gap junctions, which are established rapidly, permit exogenous NSCs to influence directly host network activity, including synchronized calcium transients with host cells in fluctuating networks. The exogenous NSCs also protect host neurons from death and reduce such signs of secondary injury as reactive astrogliosis. To determine whether gap junctions between NSCs and host cells may also mediate neuroprotection in vivo, we examined NSC transplantation in two murine models characterized by degeneration of the same cell type (Purkinje neurons) from different etiologies, namely, the nervous and SCA1 mutants. In both, gap junctions (containing connexin 43) formed between NSCs and host cells at risk, and were associated with rescue of neurons and behavior (when implantation was performed before overt neuron loss). Both in vitro and in vivo beneficial NSC effects were abrogated when gap junction formation or function was suppressed by pharmacologic and/or RNA-inhibition strategies, supporting the pivotal mediation by gap-junctional coupling of some modulatory, homeostatic, and protective actions on host systems as well as establishing a template for the subsequent development of electrochemical synaptic intercellular communication.
11.2: Efficient Deep Blue Triplet Emitters for OLEDs (2006)

Abstract Cyclometallated iridium carbene complexes are introduced as efficient blue triplet emitters. Quantum mechanical calculations have been used to design and to optimize this class of materials predominantely with respect to color coordinates and luminescence quantum yield. To complete the set of materials required for deep blue OLED devices we engineered suitable host and blocker materials for the use in combination with large triplet energy carbene emitters. These tailor‐made materials were applied to develop deep blue electroluminescent devices with excellent efficiency.
Robust, noniterative, and computationally efficient modification of van Cittert deconvolution optical figuring (1994)

A modification of van Cittert deconvolution (VCD) is introduced and shown to yield a robust, noniterative (or closed-form), and numerically efficient method of deconvolution. This modification removes the restrictions limiting the applicability of conventional VCD only to shapes and relative positions of the convolved functions for which it converges, while also avoiding the ill effects of zeros in these functions. The resulting method is computationally efficient because it is noniterative and uses the fast Fourier transform. In contrast to the convergences obtained with VCD, those obtained with this modified method are ensured by their expansion in terms of an introduced auxiliary function rather than the convolved functions. This permits both the general removal of the above limitations and arbitrarily accurate deconvolution of infinitely sampled input data even in the presence of input data noise. For discretely sampled input data the accuracy of this modification is shown to be limited only by the implicit bandwidth of the input data density. To exemplify its numerical and analytical advantages, I apply the method to computer control of optical surface figuring. I also demonstrate an intrinsic means of optimal frequency filtering of raw input data made available by this modification. The advantages of this procedure are also applicable to image restoration.
Pulsed Ultrasound Enhances the Killing of <i>Escherichia coli</i> Biofilms by Aminoglycoside Antibiotics In Vivo (2000)

Escherichia coli biofilms on two polyethylene disks were implanted subcutaneously into rabbits receiving systemic gentamicin. Ultrasound was applied for 24 h to one disk. Both disks were removed, and viable bacteria were counted. Pulsed ultrasound significantly reduced bacterial viability below that of nontreated biofilms without damage to the skin.
Temperature insensitive design of Fabry-Perot etalon (1999)

A new design of a Fabry-Perot etalon for reducing temperature dependence is proposed and demonstrated. An experiment using a 60-μm-thick etalon with a 13-nm free-spectral range at 1550-nm wavelength showed that the wavelength at resonance observed in the transmission spectrum was very stable and stayed within a range of 0.02 nm over a temperature range from 5/spl deg/C to 85/spl deg/C.
Storage, transportation, and atomization of CWF for residential applications. Final report, September 27, 1989--November 15, 1991 (1991)

This project investigated the properties and behavior with regard to handling, storage, and atomization in small-scale applications of different CWFs (coal water fuels) prepared from different parent coals and various beneficiation techniques as well as consideration for bulk storage and distribution. The CWFs that were prepared included Upper Elkhorn No. 3, Illinois No. 6, and Upper Wyodak coal cleaned by heavy media separation. Also, several CWFs were prepared with Upper Elkhorn No. 3 coal cleaned by heavy media separation with filtration, chemical cleaning, oil agglomeration, and froth flotation.
Optical properties of cyclic olefin copolymers (2001)

The optical properties of a cyclic olefin copolymer, Topas™, made by Celanese AG, are presented. This class of materials is attractive on account of their high use temperature, excellent optical transmission, low birefringence, and low moisture uptake. These materials are compared with other commonly used thermoplastics, namely, polycarbonate and polymethyl methacrylate. Finally, Topas™ is compared with a number of other optical polymers being studied for optical waveguiding applications. It is found that at 830 nm Topas™ has low losses (less than 0.5 dB/cm), so that it may be useful for datacom applications. At the telecommunication wavelength of 1550 nm the losses are in the range of 0.7 dB/cm.
Reduced Neuropeptide Y Concentrations in Suicide Brain (1992)

Neuropeptide Y (NPY) was measured in postmortem brain tissue from victims of suicide and from individuals dying a sudden natural or accidental death (controls). Concentrations of NPY-immunoreactivity were measured by radioimmunoassay in frontal cortex (BA 10), temporal cortex (BA 22), caudate nucleus, and cerebellum. Concentrations of NPY-immunoreactivity were significantly lower in postmortem frontal cortex (-14%) and caudate nucleus (-27%) from suicide victims compared with age-matched controls. A subgroup of suicides with evidence of a history of depression revealed more robust reductions in concentrations of NPY-immunoreactivity in frontal cortex and caudate nucleus, as did four individuals who died from natural causes and also were described as having a possible history of depression. Concentrations of NPY-immunoreactivity in temporal cortex and cerebellum from victims of suicide or from the subgroup of subjects with a possible history of depression were not significantly different from those of age-matched controls. We suggest there is a deficit in the brain NPY system leading to region-specific reductions in peptide concentrations in subjects who have a history of depression.
Inhibition of Subgenomic Hepatitis C Virus RNA Replication by Acridone Derivatives: Identification of an NS3 Helicase Inhibitor (2009)

We report the synthesis and structure-activity relationship (SAR) of a large series of acridones and acridone-fragment derivatives designed on the basis of the selective antihepatitis C virus (HCV) activity shown by acridone 2, previously studied as a potential antibovine viral diarrhea virus (BVDV) compound. The evaluation of their ability to inhibit the HCV replication in Huh-5-2 cells led to the identification of new, selective inhibitors. This indicates that the acridone skeleton, when properly functionalized, is a suitable scaffold to obtain potential anti-HCV agents. Interestingly, during identification of possible cellular and viral targets, it was discovered that compound 23 exerts inhibitory activity on the HCV NS3 helicase, a very promising target for the development of anti-HCV drugs.
High performance ultra-low-precision convolutions on mobile devices (2017)

Many applications of mobile deep learning, especially real-time computer vision workloads, are constrained by computation power. This is particularly true for workloads running on older consumer phones, where a typical device might be powered by a single- or dual-core ARMv7 CPU. We provide an open-source implementation and a comprehensive analysis of (to our knowledge) the state of the art ultra-low-precision (&lt;4 bit precision) implementation of the core primitives required for modern deep learning workloads on ARMv7 devices, and demonstrate speedups of 4x-20x over our additional state-of-the-art float32 and int8 baselines.
Ultra Low Density Spread Transmission (2016)

Ultra low density spread (ULDS) transmission scheme, allowing simultaneous and efficient usage of given time-frequency resources by multiple users, is presented and evaluated. The scheme is based on the special sets of LDS signatures that eliminate the need for iterative multi-user detector (MUD) in the receiver and dramatically improves reception performances, both without and with error correction codes. The ULDS transmission is particularly beneficial when the outer loop feedback to MUD is used in the receiver.
Augmenting buildings with infrared information (2002)

We describe a building information and navigation system based on Palm Pilot PDAs and a set of strong infrared transmitters, located throughout a building. The infrared senders stream localized data, thus effectively augmenting areas of space with localized information. This information can be perceived by just entering those areas with the PDA in your hand. We show that this form of augmentation of an environment can serve a multitude of purposes and requires neither the employment of classic 3D augmented reality nor to carry around wearable computers nor to wear head mounted displays.
Cholesterol homeostatic responses provide biomarkers for monitoring treatment for the neurodegenerative disease Niemann–Pick C1 (NPC1) (2014)

Niemann-Pick C1 (NPC1) disease is a rare, neurodegenerative lysosomal cholesterol storage disorder, typified by progressive cognitive and motor function impairment. Affected individuals usually succumb to the disease in adolescence. 2-Hydroxypropyl-β-cyclodextrin (HP-β-CD) has emerged as a promising intervention that reduces lipid storage and prolongs survival in NPC1 disease animal models. A barrier to the development of HP-β-CD and other treatments for NPC disease has been the lack of validated biochemical measures to evaluate efficacy. Here we explored whether cholesterol homeostatic responses resulting from HP-β-CD-mediated redistribution of sequestered lysosomal cholesterol could provide biomarkers to monitor treatment. Upon direct CNS delivery of HP-β-CD, we found increases in plasma 24(S)-HC in two independent NPC1 disease animal models, findings that were confirmed in human NPC1 subjects receiving HP-β-CD. Since circulating 24(S)-HC is almost exclusively CNS-derived, the increase in plasma 24(S)-HC provides a peripheral, non-invasive measure of the CNS effect of HP-β-CD. Our findings suggest that plasma 24(S)-HC, along with the other cholesterol-derived markers examined in this study, can serve as biomarkers that will accelerate development of therapeutics for NPC1 disease.