gebhart/patrepeval huggingface dataset:
Disruption-Tolerant Routing with Scoped Propagation of Control Information (2007)

We consider the problem of routing messages through a network with episodic connectivity without a priori knowledge of node schedules or locations. We present Steward assisted routing (StAR), an efficient loop-free routing framework that can operate in networks that are well-connected as well as in networks that exhibit intermittent connectivity; the proposed protocol uses Steward nodes to deliver data to destinations that may be partitioned from the source. We also introduce a companion protocol, scoped contact and interest propagation (SCIP), which contains mechanisms with which dissemination of routing control information for destinations of interest is scoped to a well-defined region of the network. We evaluate our protocols through simulations with four distinct mobility scenarios, including two that are generated using data traces from real networks. Our results show that StAR achieves delivery rates comparable to epidemic routing with far less signaling overhead. We also show that the addition of SCIP to StAR reduces route maintenance overhead significantly without impacting delivery rates.
The interaction of a giant planet with a disc with MHD turbulence — II. The interaction of the planet with the disc (2003)

We present a global magnetohydrodynamics (MHD) simulation of a turbulent accretion disc interacting with a giant protoplanet of 5 Jupiter masses in a fixed circular orbit. The disc model had an aspect ratio H /r = 0.1, and in the absence of the protoplanet a typical value of the Shakura-Sunyaev stress parameter = 5 10 -3 . As expected from previous work, the protoplanet was found to open and maintain a significant gap in the disc, with the interaction leading to inward migration of the protoplanet orbit on the expected time-scale. No evidence for a persistent net mass flow through the gap was found. However, this may be because an extensive inner cavity could not be formed for the model adopted.
Cerebral vascular adaptation to pregnancy and its role in the neurological complications of eclampsia (2010)

The cerebral circulation has a central role in mediating the neurological complications of eclampsia, yet our understanding of how pregnancy and preeclampsia affect this circulation is severely limited. Here, we show that pregnancy causes outward remodeling of penetrating arterioles and increased capillary density in the brain due to activation of peroxisome proliferator-activated receptor-γ (PPARγ), a transcription factor involved in cerebrovascular remodeling and highly activated in pregnancy. Pregnancy-induced PPARγ activation also significantly affected cerebral hemodynamics, decreasing vascular resistance and increasing cerebral blood flow by ∼40% in response to acute hypertension that caused breakthrough of autoregulation. These structural and hemodynamic changes in the brain during pregnancy were associated with substantially increased blood-brain barrier permeability, an effect that could promote passage of damaging proteins into the brain and cause the neurological complications of eclampsia, including seizure.
Biochemical and Biologic Characterization of Exosomes and Microvesicles as Facilitators of HIV-1 Infection in Macrophages (2012)

Exosomes and microvesicles (MV) are cell membranous sacs originating from multivesicular bodies and plasma membranes that facilitate long-distance intercellular communications. Their functional biology, however, remains incompletely understood. Macrophage exosomes and MV isolated by immunoaffinity and sucrose cushion centrifugation were characterized by morphologic, biochemical, and molecular assays. Lipidomic, proteomic, and cell biologic approaches uncovered novel processes by which exosomes and MV facilitate HIV-1 infection and dissemination. HIV-1 was "entrapped" in exosome aggregates. Robust HIV-1 replication followed infection with exosome-enhanced fractions isolated from infected cell supernatants. MV- and exosome-facilitated viral infections are affected by a range of cell surface receptors and adhesion proteins. HIV-1 containing exosomes readily completed its life cycle in human monocyte-derived macrophages but not in CD4(-) cells. The data support a significant role for exosomes as facilitators of viral infection.
Continuous Infrared Analysis of N<sub>2</sub>O in Combustion Products (1989)

Nitrous oxide (N2O) levels in the atmosphere are increasing, potentially contributing to the greenhouse effect and depletion of stratospheric ozone. From a limited data base, combustion sources have been identified as a major anthropogenic source of N2O. However, the existing data base (obtained by traditional grab sampling techniques followed by gas chromatographic analysis) is in question due to the discovery of a sampling artifact. A continuous on-line N2O analyzer would enable and facilitate the accurate characterization of combustion sources over a range of operating conditions, and also aid in the development of an appropriate sampling technique. This paper addresses the development of a continuous measurement technique, and the evaluation and initial use of a field prototype continuous N2O analyzer developed at the UCI Combustion Laboratory in cooperation with a major instrument manufacturer. The analyzer is capable of measuring N2O levels down to a few ppm. The analyzer has been evaluated and used to study the N2O emissions from a pulverized coal-fired boiler. The N2O levels found with the analyzer are substantially lower than levels previously attributed to such sources. Initial N2O measurements made with the analyzer suggest that N2O levels are not a substantial fraction of the NOX levels, as previously suggested.
Review of Rapid Thermal Annealing of Ion Implanted GaAs (1986)

Results of rapid thermal annealing (RTA) of ion implanted for times of 1–100s are reviewed. Comparison between silicon, selenium, and other donor ions is presented and the highest doping levels achieved are highlighted. P‐type dopants such as zinc, magnesium, and beryllium are also discussed, as well as the use of dual implants to enhance activation. N‐type doping levels up to have been demonstrated, whereas for p‐type doping levels approaching 1020cm−3 with little diffusion have been achieved. The less stringent requirements imposed on both the encapsulant and substrate material when RTA is used are also discussed.
A low power current sensing scheme for cmos sram (2005)

A low power current sensing scheme for CMOS SRAM is presented in this paper. The proposed scheme includes a modified current conveyor as the column selector, and a new designed low power current sense amplifier to sense the small differential current signals in data lines. The output of the sense amplifier is fed to a clock control RS latch both for power reduction and longer output valid time. This current sensing scheme is clocked asynchronously and the timing control circuits are also discussed. Simulation results show that a sensing speed with 3ns less is achieved by this scheme and the sensing speed is insensitive to both bit line and data line capacitances.
Daily energy expenditure in free-living heart failure patients (1997)

We examined the hypothesis that weight loss in heart failure patients is associated with elevated daily energy expenditure. Twelve cachectic patients [age = 73 +/- 6 yr; weight loss = 15 +/- 6 kg; body mass index (BMI) = 21 +/- 5 kg/m2], 13 noncachectic patients (age = 67 +/- 5 yr; BMI = 27 +/- 5 kg/m2), and 50 healthy elderly controls (age = 69 +/- 6 yr; BMI = 26 +/- 4 kg/m2) were studied. Daily energy expenditure and it components were measured using doubly labeled water and indirect calorimetry and body composition by dual-energy X-ray absorptiometry. Fat mass and fat-free mass were lower (P < 0.05) in cachectic patients compared with noncachectic patients and healthy controls. Daily energy expenditure was lower (P < 0.05) in cachectic patients (1,870 +/- 347 kcal/day) compared with noncachectic patients (2,349 +/- 545 kcal/day) and healthy controls (2,543 +/- 449 kcal/day). Differences in daily energy expenditure were primarily due to lower (P < 0.05) physical activity energy expenditure in cachectic (269 +/- 307 kcal/day) and noncachectic patients (416 +/- 361 kcal/day) compared with healthy controls (728 +/- 374 kcal/day). A lower (P < 0.05) resting energy expenditure was also noted in cachectic patients (1,414 +/- 210 kcal/day) compared with noncachectic patients (1,698 +/- 252 kcal/day) and healthy controls (1,561 +/- 223 kcal/day). These findings show that daily energy expenditure is not higher, but significantly lower, in cachectic heart failure patients due to lower physical activity and resting energy expenditure. These results argue against the hypothesis that an abnormally elevated daily energy expenditure is associated with weight loss in heart failure.
Arabidopsis Spermidine Synthase Is Targeted by an Effector Protein of the Cyst Nematode <i>Heterodera schachtii</i> (2009)

Cyst nematodes are sedentary plant parasites that cause dramatic cellular changes in the plant root to form feeding cells, so-called syncytia. 10A06 is a cyst nematode secretory protein that is most likely secreted as an effector into the developing syncytia during early plant parasitism. A homolog of the uncharacterized soybean cyst nematode (Heterodera glycines), 10A06 gene was cloned from the sugar beet cyst nematode (Heterodera schachtii), which is able to infect Arabidopsis (Arabidopsis thaliana). Constitutive expression of 10A06 in Arabidopsis affected plant morphology and increased susceptibility to H. schachtii as well as to other plant pathogens. Using yeast two-hybrid assays, we identified Spermidine Synthase2 (SPDS2), a key enzyme involved in polyamine biosynthesis, as a specific 10A06 interactor. In support of this protein-protein interaction, transgenic plants expressing 10A06 exhibited elevated SPDS2 mRNA abundance, significantly higher spermidine content, and increased polyamine oxidase (PAO) activity. Furthermore, the SPDS2 promoter was strongly activated in the nematode-induced syncytia, and transgenic plants overexpressing SPDS2 showed enhanced plant susceptibility to H. schachtii. In addition, in planta expression of 10A06 or SPDS2 increased mRNA abundance of a set of antioxidant genes upon nematode infection. These data lend strong support to a model in which the cyst nematode effector 10A06 exerts its function through the interaction with SPDS2, thereby increasing spermidine content and subsequently PAO activity. Increasing PAO activity results in stimulating the induction of the cellular antioxidant machinery in syncytia. Furthermore, we observed an apparent disruption of salicylic acid defense signaling as a function of 10A06. Most likely, increased antioxidant protection and interruption of salicylic acid signaling are key aspects of 10A06 function in addition to other physiological and morphological changes caused by altered polyamines, which are potent plant signaling molecules.
Real-time motion-adaptive delivery (MAD) using binary MLC: I. Static beam (topotherapy) delivery (2008)

Intra-fraction target motion hits the fundamental basis of IMRT where precise target positions are assumed. Real-time motion compensation is necessary to ensure that the same dose is delivered as planned. Strategies for conventional IMRT delivery for moving targets by dynamic multi-leaf collimators (MLC) tracking are well published. Binary MLC-based IMRT,such as TomoTherapy , requires synchronized motion of MLC, the couch and the gantry, which suggests a unique motion management strategy. Thanks to it sultra-fast leaf response and fast projection rate, real-time motion compensation for binary MLC-based IMRT is feasible. Topotherapy is a new IMRT delivery technique, which can be implemented in commercial helical TomoTherapy machines using only fixed gantry positions. In this paper, we present a novel approach for TopoTherapy delivery that adjusts for moving targets without additional hardware and control requirement. This technique uses the planned leaf sequence but rearranges the projection and leaf indices. It does not involve time-consuming operations, such as reoptimization. Unlike gating or breath hold-based methods, this technique can achieve nearly a 100% duty cycle with little breath control. Unlike dynamic MLC-based tracking methods, this technique requires neither the whole target motion trajectory nor the velocity of target motion. Instead, it only requires instantaneous target positions, which greatly simplifies the system implementation. Extensive simulations, including the worst-case scenarios, validated the presented technique to be applicable to relatively regular or mild irregular respirations. The delivered dose conforms well to the target, and significant margin reduction can be achieved provided that accurate, real-time tumor localization is available.
Effect of spatio-energy correlation in PCD due to charge sharing, scatter, and secondary photons (2017)

Charge sharing, scatter and fluorescence events in a photon counting detector (PCD) can result in multiple counting of a single incident photon in neighboring pixels. This causes energy distortion and correlation of data across energy bins in neighboring pixels (spatio-energy correlation). If a “macro-pixel” is formed by combining multiple small pixels, it will exhibit correlations across its energy bins. Charge sharing and fluorescence escape are dependent on pixel size and detector material. Accurately modeling these effects can be crucial for detector design and for model based imaging applications. This study derives a correlation model for the multi-counting events and investigates the effect in virtual non-contrast and effective monoenergetic imaging. Three versions of 1 mm<sup>2</sup> square CdTe macro-pixel were compared: a 4×4 grid, 2×2 grid, or 1×1 composed of pixels with side length 250 μm, 500 μm, or 1 mm, respectively. The same flux was applied to each pixel, and pulse pile-up was ignored. The mean and covariance matrix of measured photon counts is derived analytically using pre-computed spatio-energy response functions (SERF) estimated from Monte Carlo simulations. Based on the Cramer-Rao Lower Bound, a macro-pixel with 250×250 μm<sup>2</sup> sub-pixels shows ~2.2 times worse variance than a single 1 mm<sup>2</sup> pixel for spectral imaging, while its penalty for effective monoenergetic imaging is <10% compared to a single 1 mm<sup>2</sup> pixel.
Health Mashups (2013)

People now have access to many sources of data about their health and wellbeing. Yet, most people cannot wade through all of this data to answer basic questions about their long-term wellbeing: Do I gain weight when I have busy days? Do I walk more when I work in the city? Do I sleep better on nights after I work out? We built the Health Mashups system to identify connections that are significant over time between weight, sleep, step count, calendar data, location, weather, pain, food intake, and mood. These significant observations are displayed in a mobile application using natural language, for example, “You are happier on days when you sleep more.” We performed a pilot study, made improvements to the system, and then conducted a 90-day trial with 60 diverse participants, learning that interactions between wellbeing and context are highly individual and that our system supported an increased self-understanding that lead to focused behavior changes.
Multilayered Blood Capillary Analogs in Biodegradable Hydrogels for In Vitro Drug Permeability Assays (2012)

Abstract Blood capillaries are crucial for the biological evaluation of drug diffusion to target tissues, and the penetration of cancer cells or viruses. Since most capillaries have a bilayered structure consisting of a monolayer of endothelial cells (ECs) and surrounding smooth muscle cells (SMCs), the in vitro reconstruction of this bilayered structure is a key challenge for pharmaceutical and biomedical applications. Here, a unique technology to construct size, length, orientation, and layer‐number controllable blood capillary networks in biodegradable hydrogels is reported. Uniaxial microchannels are prepared inside biodegradable hydrogels by the simple extraction of silica capillary tubes. The channel size, length, and distance of the uniaxial channels are easily controlled by altering these parameters of the silica tubes. The inner surfaces of the channels are successfully covered by bilayered structures consisting of ECs and SMCs by a hierarchical cell manipulation technique. Notably, serum albumin, which has an approximately 8 nm size, cannot penetrate this capillary wall during several hours of incubation due to the high blood vessel wall barrier property. This suggests a successful reconstruction of multilayered blood capillary networks possessing similar barrier function as native blood capillaries. Moreover, these capillary networks can be completely collected by the selective degradation of the surrounding hydrogels. This technique will be an innovative and versatile approach for in vitro permeability assays of drugs, drug delivery carriers, and cancer cells.
Cerebral Ischemia and Infarction From Atheroemboli <100 μm in Size (2003)

Background and Purpose— To determine the importance of emboli not trapped by carotid angioplasty filtration devices, we examined fragments <100 μm released with ex vivo angioplasty and asked if fragment composition and size correlated with brain injury. Methods— Human carotid plaques (21) were excised en bloc, and ex vivo carotid angioplasty was performed. Eight plaques were selected as either highly calcified (4) or highly fibrotic (4) by high-resolution MRI (200 μm 3 ). Fragments were counted by a Coulter counter. Before injection into male Sprague-Dawley rats, fragments from calcified and fibrotic plaques were sized with 60-, 100-, and 200-μm filters. Brain ischemia and infarction were assessed by MRI scans (7-T small-bore magnet) and by immunohistologic staining for HSP70 and NueN. Results— All 5 animals injected with 100- to 200-μm calcified fragments had infarctions. One was lethal. After injection of 60- to 100-μm calcified fragments, 7 of 12 animals had cerebral infarctions, whereas only 1 of 11 had infarctions with fibrous fragments ( P <0.02). HSP70 staining showed that ischemia was more common and more extensive than infarction. Ischemia was found in 10 of 12 animals after injection of calcified fragments and in 9 of 11 after injection of fibrous fragments. The mean number of 60- to 100-μm fragments released was 375±510; the mean number of 20- to 60-μm fragments was 34 196 (range, 2230 to 186 927). Conclusions— Hundreds of thousands of microemboli can be shed during carotid angioplasty. Fragments from calcified plaques cause greater levels of infarction than fragments from fibrous plaques, although ischemia is common with both fragment types.
Encapsulant materials for flip-chip attach (2002)

The properties of the underfill and its characteristics, before and after curing, have a significant impact on the assembly process and the reliability of the product. Some of these are flow characteristics, filler settling, filler particle size, voiding, glass transition, coefficient of thermal expansion, adhesion strength, modulus, fracture toughness, etc. The time associated with 'underfilling' a flip chip assembly has to be 'optimized' in order to improve throughput without sacrificing assembly reliability. It depends on a variety of parameters such as the die size, the encapsulant material type, standoff height, etc. Therefore, it is critical to develop an understanding of these parameters and their effect on dispensing time. This paper provides a review of the critical factors that influence the development and implementation of an effective and efficient underfill process for flip chip assemblies. The flow properties (flow front, filler settling, and voiding) of an encapsulant not only have an impact on the dispensing time, but also significantly influence the reliability of the flip-chip assembly. This research studied the effect of encapsulant material type and standoff height on the time taken to flow to specified distances. These factors and the interactions between them were analyzed using statistically designed flow experiments. The effect of these input factors on the flow front, filler settling, and voiding have been considered. A detailed understanding of the material's flow properties and an effective estimate of the encapsulant's flow time can help to develop a robust process.
Activation of G551D CFTR channel with MPB-91: regulation by ATPase activity and phosphorylation (2001)

We have designed and synthesized benzo[c]quinolizinium derivatives and evaluated their effects on the activity of G551D cystic fibrosis transmembrane conductance regulator (CFTR) expressed in Chinese hamster ovary and Fisher rat thyroid cells. We demonstrated, using iodide efflux, whole cell patch clamp, and short-circuit recordings, that 5-butyl-6-hydroxy-10-chlorobenzo[c]quinolizinium chloride (MPB-91) restored the activity of G551D CFTR (EC(50) = 85 microM) and activated CFTR in Calu-3 cells (EC(50) = 47 microM). MPB-91 has no effect on the ATPase activity of wild-type and G551D NBD1/R/GST fusion proteins or on the ATPase, GTPase, and adenylate kinase activities of purified NBD2. The activation of CFTR by MPB-91 is independent of phosphorylation because 1) kinase inhibitors have no effect and 2) the compound still activated CFTR having 10 mutated protein kinase A sites (10SA-CFTR). The new pharmacological agent MPB-91 may be an important candidate drug to ameliorate the ion transport defect associated with CF and to point out a new pathway to modulate CFTR activity.
Panel of Prototypical Raltegravir-Resistant Infectious Molecular Clones in a Novel Integrase-Deleted Cloning Vector (2009)

We created an HIV-1 cloning vector, pNL4.3DeltaIN, to generate recombinant infectious molecular clones for analysis of patient-derived HIV-1 integrase coding regions. Using this vector, we constructed a panel of clinically derived viruses with the canonical patterns of raltegravir resistance mutations and submitted the panel to the NIH AIDS Research and Reference Reagent Program. Investigational integrase inhibitors with activity against these clones are likely to retain activity against the most clinically relevant raltegravir-resistant variants.
Remarkable longevity and stress resistance of nematode PI3K‐null mutants (2007)

The great majority of lifespan-augmenting mutations were discovered in the nematode Caenorhabditis elegans. In particular, genetic disruption of insulin-like signaling extends longevity 1.5- to 3-fold in the nematode, and to lesser degrees in other taxa, including fruit flies and mice. C. elegans strains bearing homozygous nonsense mutations in the age-1 gene, which encodes the class-I phosphatidylinositol 3-kinase catalytic subunit (PI3K(CS)), produce progeny that were thought to undergo obligatory developmental arrest. We now find that, after prolonged developmental times at 15-20 degrees C, they mature into extremely long-lived adults with near-normal feeding rates and motility. They survive to a median of 145-190 days at 20 degrees C, with nearly 10-fold extension of both median and maximum adult lifespan relative to N2DRM, a long-lived wild-type stock into which the null mutant was outcrossed. PI3K-null adults, although a little less thermotolerant, are considerably more resistant to oxidative and electrophilic stresses than worms bearing normal or less long-lived alleles. Their unprecedented factorial gains in survival, under both normal and toxic environments, are attributed to elimination of residual and maternally contributed PI3K(CS) or its products, and consequent modification of kinase signaling cascades.