gebhart/patrepeval huggingface dataset:
Printed Arrays of Aligned GaAs Wires for Flexible Transistors, Diodes, and Circuits on Plastic Substrates (2006)

GaAs – your flexible friend! Aligned arrays of GaAs wires with integrated ohmic contacts generated from high-quality, single-crystalline wafers via photolithography and anisotropic chemical etching provide a promising class of material for transistors, Schottky diodes, logic gates (see image), and even more complex circuits on flexible plastic substrates. These devices exhibit excellent electronic and mechanical characteristics, which are both important to the emerging area of low-cost, large-area flexible electronics, often referred to as macroelectronics. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2006/z500528_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.
Synthesis of carbocyclic NAD+ containing a methylenebisphosphonate linkage for the investigation of ADP-ribosyl cyclase (1996)

A stereospecific synthesis of carbocyclic NAD+ incorporating a methylenebisphosphonatelinkage in place of the natural pyrophosphate gives an analogue 4 of the natural coenzyme NAD+ 3a designed to act as an inhibitor of ADP-ribosyl cyclase and to resist non-specific phosphatase degradation.
Development of a Delayed-Type Hypersensitivity (DTH) Model in the Cynomolgus Monkey (2012)

Although a T-dependent antibody response (TDAR) assay is generally recommended as the first-line immune function assay in nonclinical immunotoxicity evaluation, second-line assays such as delayed-type hypersensitivity (DTH) to measure cell-mediated responses can provide helpful additional information. In this study, male Cynomolgus monkeys were injected intramuscularly either once or twice with 1 mg Keyhole Limpet Hemocyanin (KLH) or twice with a commercially available tetanus vaccine (40 IU tetanus toxoid + 0.06 mg aluminum hydroxide). All animals were subsequently challenged by intradermal injections of the same antigen or aluminum hydroxide after 4, 6 and 8 weeks. Clinical reactions at the injection sites were scored 24, 48 and 72 h post challenge. Skin biopsies were taken on completion of the observation period after each challenge for standard histological examination and immunolabeling using CD3 (T lymphocytes), CD19 (B lymphocytes) and CD68 (macrophages) antibodies. Tetanus toxoid induced stronger clinical reactions than KLH, whereas aluminum hydroxide induced no clinical reaction. Perivascular mononuclear cell infiltrates, a histopathological finding consistent with a DTH reaction, were seen after all challenges with tetanus toxoid or KLH, but not with aluminum hydroxide. Immunohistochemistry evidenced the presence of T lymphocytes and macrophages within these infiltrates. These results suggest that tetanus toxoid adjuvanted with aluminum hydroxide can induce a consistent DTH response for use as a model of cell-mediated response in Cynomolgus monkeys.
Disordered Cellular Migration and Angiogenesis in cd39- Null Mice (2001)

Our findings demonstrate a role for NTPDase1 and phosphohydrolysis of extracellular nucleotides in the regulation of the cellular infiltration and new vessel growth in a model of angiogenesis.
Potent VEGF blockade causes regression of coopted vessels in a model of neuroblastoma (2002)

Vascular endothelial growth factor (VEGF) plays a key role in human tumor angiogenesis. We compared the effects of inhibitors of VEGF with different specificities in a xenograft model of neuroblastoma. Cultured human neuroblastoma NGP-GFP cells were implanted intrarenally in nude mice. Three anti-VEGF agents were tested: an anti-human VEGF(165) RNA-based fluoropyrimidine aptamer; a monoclonal anti-human VEGF antibody; and VEGF-Trap, a composite decoy receptor based on VEGFR-1 and VEGFR-2 fused to an Fc segment of IgG1. A wide range of efficacy was observed, with high-dose VEGF-Trap causing the greatest inhibition of tumor growth (81% compared with controls). We examined tumor angiogenesis and found that early in tumor formation, cooption of host vasculature occurs. We postulate that this coopted vasculature serves as a source of blood supply during the initial phase of tumor growth. Subsequently, control tumors undergo vigorous growth and remodeling of vascular networks, which results in disappearance of the coopted vessels. However, if VEGF function is blocked, cooption of host vessels may persist. Persistent cooption, therefore, may represent a novel mechanism by which neuroblastoma can partly evade antiangiogenic therapy and may explain why experimental neuroblastoma is less susceptible to VEGF blockade than a parallel model of Wilms tumor. However, more effective VEGF blockade, as achieved by high doses of VEGF-Trap, can lead to regression of coopted vascular structures. These results demonstrate that cooption of host vasculature is an early event in tumor formation, and that persistence of this effect is related to the degree of blockade of VEGF activity.
NH3 Volatilization from Aboveground Plants of Winter Wheat during Late Growing Stages (2003)

Ammonia volatilized from aboveground parts of winter wheat was collected with an enclosure growth chamber and measured from jointing to maturing stage. The results showed that ammonia released from unfertilized plants grown in high and low fertility soils remained at low rates of 2.3 and 0.9μg NH3 40 plant^(-1) h^(-1) respectively at late filling stage. However, fertilized plants rapidly increased the rates to 43.4 and 52.2μg NH3 40 plant^(-1) h^(-1) in the high and low fertility soils, respectively, at the same period. The released a-mount was different in different parts of plants. At filling stage, lower senescing stems and leaves volatilized more ammonia than upper parts, i.e., ears and flag leaves that grew normally, with an average of 1.4 and 0.7μg NH3 20 plant^(-1) h^(-1) respectively, strongly suggesting that it was the senile organs that released large amounts of ammonia. At the grain filling stage, shortage of water supply (drought stress) reduced ammonia volatilization. The average rate of ammonia released under water stress was 0.9μg NH3 40 plant^(-1) h^(-1), but 1.2μg NH3 40 plant^(-1) h^(-1) with moderate water supply. Application of N together with P fertilizer resulted in a higher ammonia volatilization than N fertilization alone at the maturing stage. The average rate released was 135.3μg NH3 40 plant^(-1) h^(-1) when 0.4 g N and 0.13 g P had been added to per kg soil, while 33.7μg when 0.4 g N added alone. Ammonia volatilization from plants was closely related with plant biomass and N uptake; P fertilization increased plant biomass and N uptake and therefore increased its release.
RNA structure determination by solid-state NMR spectroscopy (2015)

Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize—and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies.
Automated worm fingerprinting (2004)

Network worms are a clear and growing threat to the security of today’s Internet-connected hosts and networks. The combination of the Internet’s unrestricted connectivity and widespread software homogeneity allows network pathogens to exploit tremendous parallelism in their propagation. In fact, modern worms can spread so quickly, and so widely, that no human-mediated reaction can hope to contain an outbreak. In this paper, we propose an automated approach for quickly detecting previously unknown worms and viruses based on two key behavioral characteristics – a common exploit sequence together with a range of unique sources generating infections and destinations being targeted. More importantly, our approach – called “content sifting ” – automatically generates precise signatures that can then be used to filter or moderate the spread of the worm elsewhere in the network. Using a combination of existing and novel algorithms we have developed a scalable content sifting implementation with low memory and CPU requirements. Over months of active use at UCSD, our Earlybird prototype system has automatically detected and generated signatures for all pathogens known to be active on our network as well as for several new worms and viruses which were unknown at the time our system identified them. Our initial experience suggests that, for a wide range of network pathogens, it may be practical to construct fully automated defenses – even against so-called “zero-day” epidemics. 1
Linear velocity and acceleration estimation of 3 DOF haptic interfaces (2008)

Velocity and acceleration of the end effector of a haptic interface are required for haptic rendering in many aspects such as software damping, friction force rendering, and position control, etc. However, due to limited sensor resolution, non-linearity of forward kinematics, high maneuverability of human arm/hand, and high sampling rate requirement, getting a precise and robust velocity and acceleration estimation is very challenging. In this paper, an adaptive 4-state Kalman filter to estimate the velocity and the acceleration of the end effector is proposed considering that the human arm/hand trajectory has at least 5 non-zero derivatives and the skilled movements follows the constrained minimum jerk trajectory planning. The preliminary simulation results show the effectiveness of the proposed method.
The Role of Uncertainty, Awareness, and Trust in Visual Analytics (2015)

Visual analytics supports humans in generating knowledge from large and often complex datasets. Evidence is collected, collated and cross-linked with our existing knowledge. In the process, a myriad of analytical and visualisation techniques are employed to generate a visual representation of the data. These often introduce their own uncertainties, in addition to the ones inherent in the data, and these propagated and compounded uncertainties can result in impaired decision making. The user's confidence or trust in the results depends on the extent of user's awareness of the underlying uncertainties generated on the system side. This paper unpacks the uncertainties that propagate through visual analytics systems, illustrates how human's perceptual and cognitive biases influence the user's awareness of such uncertainties, and how this affects the user's trust building. The knowledge generation model for visual analytics is used to provide a terminology and framework to discuss the consequences of these aspects in knowledge construction and though examples, machine uncertainty is compared to human trust measures with provenance. Furthermore, guidelines for the design of uncertainty-aware systems are presented that can aid the user in better decision making.
Antisera inhibiting mammalian cell spreading and possible cell surface antigens involved. (1980)

Antiserum against a rat neuronal tumor cell line (B103) has been prepared in rabbit by intravenous injection of live cells. This immune serum (anti-B103) precipitates a few cell surface proteins recognizable by two-dimensional gel electrophoresis as common radioiodinatable spots in 15 different rat neural cell lines and in mouse and rat fibroblast cell lines. The apparent molecular weight of one major common protein (II4) is estimated by SDS gel electrophoresis to be somewhere between 80,000 and 90,000 and another protein (I3) to be 120,000. These two proteins are consistently recognized in various cell lines by this antiserum. Furthermore, at a 1:20 dilution, this serum causes monolayer cells to round up usually within 0.5 h and detach from the plate within 3 h. It also inhibits spreading of freshly plated cells. These effects of the antiserum are reversible. Upon absorption of the antiserum with cells (e.g., absorbed with a glial cell line, B27), the serum no longer causes the rounding up of the monolayer cells, it does not inhibit cell spreading, and it does not immune-precipitate the two common proteins from the cell surface of various cell lines. Antisera against several other rat cell lines also precipitate the same common proteins (II4 and I3) from the cell surface and prevent cell spreading. These data suggest that the antibody acts first at the cell surface and then inhibits cell spreading or rounding up of spread cells. The consistent pattern of the immunoprecipitated cell surface proteins on the two-dimensional gel electrophoresis makes these two common surface proteins (II4 or I3 or both) possible candidates for target proteins to which the antibody binds. Thus, they may play a critical role in cell spreading.
Odd even shifts in SIMD hypercubes (1990)

A linear-time algorithm is developed to perform all odd (even) length circular shifts of data in an SIMD (single-instruction-stream, multiple-data-stream) hypercube. As an application, the algorithm is used to obtain an O(M/sup 2/+log N) time and O(1) memory per processor algorithm to compute the two-dimensional convolution of an N*N image and an M*M template on an N/sup 2/ processor SIMD hypercube. This improves the previous best complexity of O(M/sup 2/ log M+log N).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Empirical determination of the electroabsorption coefficient in semiconductors (1993)

On the basis of the integral formula of Rees relating the electroabsorption coefficient to the zero-field absorption coefficient, scaling rules for the electroabsorption coefficient are obtained. These rules allow the spectral and field dependence of the electroabsorption coefficient near the fundamental band edge to be obtained. They also allow the identification of trends, thus impacting on the choice of materials and design of optoelectronic devices.
Ironing-Out Mechanisms of Neuronal Injury under Hypoxic–Ischemic Conditions and Potential Role of Iron Chelators as Neuroprotective Agents (2000)

Iron is the most abundant transition metal in the brain, where it functions as an important cofactor in a host of vital metabolic processes and plays an absolutely essential role in cell viability. Free iron is also very toxic when present in high concentrations, thus placing this essential metal at the core of neurotoxic injury in a number of neurological disorders. The pivotal role of iron in cellular homeostasis, including its latent toxicity, necessitates a tight regulation of iron metabolism. Oxygen and iron appear to play an important role in iron homeostasis. They appear to exert their homeostatic role by modulating the proteins involved in a complex interplay between iron sensing, transport, and storage. These key regulatory proteins include ferritin (intracellular storage), transferrin (extracellular transport), transferrin receptor, and iron regulatory protein (sensor of intracellular iron concentration). The interplay of iron and oxygen is most intriguing in the setting of stroke, where hypoxia and free iron appear to interact in causing the subsequent neuronal death.
Expression of the mouse Gli and Ptc genes is adjacent to embryonic sources of hedgehog signals suggesting a conservation of pathways between flies and mice (1997)

The three mouse Gli genes are putative transcription factors which are the homologs of cubitus interruptus (ci) in Drosophila. Along with the gene patched (Ptc), ci has been implicated in the hedgehog (Hh) signal transduction pathway. To assess the role of Gli in embryogenesis, we compared its expression with that of Ptc and Hh family members in mouse. We found that Gli and Ptc are expressed in similar domains in diverse regions of the developing mouse embryo and these regions are adjacent to Hh signals. We also show that Gli is expressed ectopically along with Ptc and Shh in Strong's luxoid mutant mice. These results are consistent with conservation of the Hh signal transduction pathway in mice with Gli potentially mediating Hh signaling in multiple regions of the developing embryo.
Recognition by restriction endonuclease EcoRI of deoxyoctanucleotides containing modified sugar moieties (1984)

The deoxyribooctanucleotide d(G-G-A-A-T-T-C-C), containing the recognition sequence for EcoRI, d(G-A-A-T-T-C), and analogs containing modified sugar moieties were tested for their activity in cleavage with EcoRI. These analogs, with replacement in the third position from the 5' end, were synthesized using 9-beta-D-arabinosyladenine (aA), 2'-deoxy-2'-fluoroadenosine (Afl) and adenosine (rA). Duplex formation by the three analogs was confirmed by measurements of ultraviolet/temperature profiles. It was found that EcoRI cleaved these duplexes less efficiently than d(G-G-A-A-T-T-C-C). The adenosine-containing analog d(G-G)-rA-d(A-T-T-C-C) was cleaved much more slowly than d(G-G)-aA-d(A-T-T-C-C) and d(G-G-Afl-A-T-T-C-C). The corresponding ribooctamer G-G-A-A-U-U-C-C showed a higher melting temperature than the deoxyoctamers but its duplex was not cleaved by this enzyme. An analog with 2'-deoxy-2'-fluoroguanosine at the second position was cleaved by the endonuclease faster than the natural deoxyoctamer.
Cu(II) Potentiation of Alzheimer Aβ Neurotoxicity (1999)

Oxidative stress markers as well as high concentrations of copper are found in the vicinity of A amyloid deposits in Alzheimer's disease. The neurotoxicity of A in cell culture has been linked to H 2 O 2 generation by an unknown mechanism. We now report that Cu(II) markedly potentiates the neurotoxicity exhibited by A in cell culture. The potentiation of toxicity is greatest for A1-42 > A1-40 > > mouse/rat A1-40, corresponding to their relative capacities to reduce Cu(II) to Cu(I), form H 2 O 2 in cell-free assays and to exhibit amyloid pathology. The copper complex of A1-42 has a highly positive formal reduction potential (500 -550 mV versus Ag/AgCl) characteristic of strongly reducing cuproproteins. These findings suggest that certain redox active metal ions may be important in exacerbating and perhaps facilitating A-mediated oxidative damage in Alzheimer's disease.
Synapse-Forming Axons and Recombinant Agrin Induce Microprocess Formation on Myotubes (2001)

We examined cell-surface behavior at nerve-muscle contacts during synaptogenesis in cocultures of rat ventral spinal cord (VSC) neurons and myotubes. Developing synapses in 1-d-old cocultures were identified by the presence of axon-induced acetylcholine receptor (AChR) aggregation. Identified regions were then examined by transmission and scanning electron microscopy. The myotube surface near contacts with axons that induced AChR aggregation typically displayed ruffles, microvilli, and filopodia (microprocesses), indicating motility of the myotube surface. At some of these contact sites microprocesses were wrapped around the axon, resulting in the partial or total "submersion" of the axon within the myotube contours. Sites of myotube contact with somata and dendrites of the same neurons showed much less evidence of motility and surface interaction than sites of contact with axons. Moreover, the distance between opposed membranes of axons and myotubes was smaller than between dendrites or somata and myotubes, suggesting stronger adhesion of axons. These results suggest polarized expression of molecules involved in the induction of microprocess formation and adhesion in developing VSC neurons. We therefore tested the ability of agrin, which is preferentially secreted by axons, to induce microprocess formation in myotubes. Addition of recombinant C-terminal agrin to culture medium resulted in formation of microprocesses within 3 hr. Myotubes transfected with full-length rat agrin constructs displayed numerous filopodia, as revealed by fluorescence microscopy. The results suggest that the induction of muscle cell surface motility may be linked to the signaling processes that trigger the initial formation of the neuromuscular junction.
Microfluidic waves (2011)

The propagation of pressure waves in fluidic channels with elastic covers is discussed in view of applications to flow control in microfluidic devices. A theory is presented which describes pressure waves in the fluid that are coupled to bending waves in the elastic cover. At low frequencies, the lateral bending of the cover dominates over longitudinal bending, leading to propagating, non-dispersive longitudinal pressure waves in the channel. The theory addresses effects due to both the finite viscosity and compressibility of the fluid. The coupled waves propagate without dispersion, as long as the wave length is larger than the channel width. It is shown that in channels of typical microfluidic dimensions, wave velocities in the range of a few 10 m s(-1) result if the channels are covered by films of a compliant material such as PDMS. The application of this principle to design microfluidic band pass filters based on standing waves is discussed. Characteristic frequencies in the range of a few kHz are readily achieved with quality factors above 30.
Protease inhibitors derived from elafin and SLPI and engineered to have enhanced specificity towards neutrophil serine proteases (2009)

The secretory leukocyte protease inhibitor (SLPI), elafin, and its biologically active precursor trappin-2 are endogeneous low-molecular weight inhibitors of the chelonianin family that control the enzymatic activity of neutrophil serine proteases (NSPs) like elastase, proteinase 3, and cathepsin G. These inhibitors may be of therapeutic value, since unregulated NSP activities are linked to inflammatory lung diseases. However SLPI inhibits elastase and cathepsin G but not proteinase 3, while elafin targets elastase and proteinase 3 but not cathepsin G. We have used two strategies to design polyvalent inhibitors of NSPs that target all three NSPs and may be used in the aerosol-based treatment of inflammatory lung diseases. First, we fused the elafin domain with the second inhibitory domain of SLPI to produce recombinant chimeras that had the inhibitory properties of both parent molecules. Second, we generated the trappin-2 variant, trappin-2 A62L, in which the P1 residue Ala is replaced by Leu, as in the corresponding position in SLPI domain 2. The chimera inhibitors and trappin-2 A62L are tight-binding inhibitors of all three NSPs with subnanomolar K(i)s, similar to those of the parent molecules for their respective target proteases. We have also shown that these molecules inhibit the neutrophil membrane-bound forms of all three NSPs. The trappin-2 A62L and elafin-SLPI chimeras, like wild-type elafin and trappin-2, can be covalently cross-linked to fibronectin or elastin by a tissue transglutaminase, while retaining their polypotent inhibition of NSPs. Therefore, the inhibitors described herein have the appropriate properties to be further evaluated as therapeutic anti-inflammatory agents.