gebhart/patrepeval huggingface dataset:
Generalized Analytical Solution for Reservoir Problems With Multiple Wells and Boundary Conditions (2006)

Abstract We present a set of new analytical solutions to the single layer reservoir problem, both in real time and Laplace space. The solutions are derived assuming a cuboid shaped reservoir using a method of integral transforms. The method can be applied to calculate the pressure as a function of position and time when using any continuous function to describe the production rate of a point source. Successive integration of the point source solution can be performed to calculate the average bottom hole pressure of a well. These equations are applicable to partially penetrating vertical, horizontal and fractured wells and take into account superposition effects in multi-well and multi-rate scenarios. Notably, regarding fractured wells, we are able to accurately model the case of a finite conductivity fracture with non-Darcy flow as well as those of infinite conductivity. The generality of our method allows any continuous function of position and time to be used to treat either pressures or fluid fluxes on the boundaries. Also, using solutions in Laplace space we are able to model naturally fractured reservoirs, wellbore storage, non-Darcy D-factors as well as constant well pressure production, also all within a full field multi-well scenario. Our method, therefore, provides a powerful alternative to simulation in terms of reservoir modeling. We present a comparison of our solutions with that generated using a commercial finite difference simulator for a variety of problems in terms of accuracy and speed. We find amazing accuracy with massive gains (factors&gt;300) in CPU times for fracture problems in particular.
Computational Studies on Acquisition and Adaptation of Ocular Following Responses Based on Cerebellar Synaptic Plasticity (2002)

To investigate how cerebellar synaptic plasticity guides the acquisition and adaptation of ocular following response (OFR), a large-scale network model was developed. The model includes the cerebral medial superior temporal area (MST), Purkinje cells (P cells) of the ventral paraflocculus, the accessory optic and climbing fiber systems, the brain stem oculomotor network, and the oculomotor plant. The model reconstructed temporal profiles of both firing patterns of MST neurons and P cells and eye movements. Model MST neurons (n = 1,080) were set to be driven by retinal error and exhibited 12 preferred directions, 30 preferred velocities, and 3 firing waveforms. Correspondingly, each model P cell contained 1,080 excitatory synapses from granule cell axons (GCA) and 1,080 inhibitory synapses. P cells (n = 40) were classified into four groups by their laterality (hemisphere) and by preferred directions of their climbing fiber inputs (CF) (contralateral or upward). The brain stem neural circuit and the oculomotor plant were modeled on the work of Yamamoto et al. The initial synaptic weights on the P cells were set randomly. At the beginning, P cell simple spikes were not well modulated by visual motion, and the eye was moved only slightly by the accessory optic system. The synaptic weights were updated according to integral-differential equation models of physiologically demonstrated synaptic plasticity: long-term depression and long-term potentiation for GCA synapses and rebound potentiation for inhibitory synapses. We assumed that maximum plasticity was induced when GCA inputs preceded CF inputs by 200 ms. After more than 10,000 presentations of ramp-step visual motion, the strengths of both the excitatory and inhibitory synapses were modified. Subsequently, the simple spike responses became well developed, and ordinary OFRs were acquired. The preferred directions of simple spikes became the opposite of those of CFs. Although the model MST neurons were set to possess a wide variety of firing characteristics, the model P cells acquired only downward or ipsilateral preferred directions, high preferred velocities and stereotypical firing waveforms. Therefore the drastic transition of the neural representation from the population codes in the MST to the firing-rate codes of simple spikes were learned at the GCA-P cell synapses and inhibitory cells-P cell synapses. Furthermore, the model successfully reproduced the gain- and directional-adaptation of OFR, which was demonstrated by manipulating the velocity and direction of visual motion, respectively. When we assumed that synaptic plasticity could only occur if CF inputs preceded GCA inputs, the ordinary OFR were acquired but neither the gain-adaptation nor the directional adaptation could be reproduced.
B7‐1/2, but not PD‐L1/2 molecules, are required on IL‐10‐treated tolerogenic DC and DC‐derived exosomes for <i>in vivo</i> function (2009)

Costimulatory molecules, such as B7-1/2 and PD-L1/2 play an important role in the function of APC. The regulation of the surface levels of costimulatory molecules is one mechanism by which APC maintain the balance between tolerance and immunity. We examined the contributions of B7-1/2 and PD-L1/2 to the function of IL-10-treated, immunosuppressive DC as well as therapeutic exosomes derived from these DC. IL-10 treatment of DC significantly downregulated surface expression of MHC II, B7-1, B7-2, and decreased levels of MHC I and PD-L2. IL-10 treatment of DC resulted in a modified costimulatory profile of DC-secreted exosomes with a reduction in B7-1, PD-L1 and PD-L2. We further demonstrate that absence of B7-1 or B7-2 on donor DC results in a loss of ability of IL-10-treated DC and their exosomes to suppress the delayed-type hypersensitivity response, whereas IL-10-treated DC deficient in PD-L1/2 as well as their secreted exosomes retained the ability to suppress delayed-type hypersensitivity responses. We conclude that B7-1 and B7-2, but not PD-L1 and PD-L2, on IL-10-treated DC and DC-derived exosomes play a critical role in immunosuppressive functions of both DC and exosomes.
PHASE-BASED SEGMENTATION OF CELLS FROM BRIGHTFIELD MICROSCOPY (2007)

Segmentation of transparent cells in brightfield microscopy images could facilitate the quantitative analysis of corresponding fluorescence images. However, this presents a challenge due to irregular morphology and weak intensity variation, particularly in ultra-thin regions. A boundary detection technique is applied to a series of variable focus images whereby a level set contour is initialised on a defocused image with improved intensity contrast, and subsequently evolved towards the correct boundary using images of improving focus. Local phase coherence is used to identify features within the images, driving contour evolution particularly in near-focus images which lack intensity contrast. Preliminary results demonstrate the effectiveness of this approach in segmenting the main cell body regions
How to Use a Monte Carlo Study to Decide on Sample Size and Determine Power (2002)

Abstract A common question asked by researchers is, "What sample size do I need for my study?" Over the years, several rules of thumb have been proposed. In reality there is no rule of thumb that applies to all situations. The sample size needed for a study depends on many factors, including the size of the model, distribution of the variables, amount of missing data, reliability of the variables, and strength of the relations among the variables. The purpose of this article is to demonstrate how substantive researchers can use a Monte Carlo study to decide on sample size and determine power. Two models are used as examples, a confirmatory factor analysis (CFA) model and a growth model. The analyses are carried out using the Mplus program (Muthén& Muthén 1998).
Novel Metabolic Pathways of p-n-Nonylphenol Catalyzed by Cytochrome P450 and Estrogen Receptor Binding Activity of New Metabolites (2007)

Nonylphenol, which is used industrially as a surfactant, is an endocrine-disrupting chemical (EDC) which has estrogenic activity. The novel biotransformation of nonylphenol was investigated, based on our previously reported ipso-metabolism of para-substituted phenols by cytochrome P450 (P450). Three novel metabolites of nonylphenol, i.e., nonylquinol, 4'-hydroxynonanophenone (CO-NP) as benzyl-oxidized nonylphenol, and hydroquinone, were detected in a rat liver microsome reaction mixture. On the other hand, production of 1-(4'-hydroxyphenyl)nonan-1-ol (OH-NP), namely benzyl-hydroxylated nonylphenol, was detected in a human liver microsome reaction mixture. The formation of all these metabolites was suppressed by the addition of P450 inhibitor. This showed that all nonylphenol metabolism was catalyzed by P450. To identify which P450 isoenzyme is involved in each reaction, fourteen human P450 (CYP) isozymes, CYP1A1, 1A2, 2A6, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 3A4, 3A5, 3A7, and CYP4A11, were examined. CYP1A1, 1A2, and CYP2B6 effectively catalyzed the production of nonylquinol. CYP2B6 also catalyzed the benzyl-hydroxylation to give OH-NP. Hydroquinone was formed mainly from OH-NP, not via CO-NP. We examined the estrogenic activity of these new metabolites by estrogen receptor (ER)-binding reporter gene assay. Nonylquinol, OH-NP and hydroquinone have no ER-binding activity. However, CO-NP showed the same level of estrogen receptor binding activity as nonylphenol. Moreover, the amount of CO-NP formed was small. Therefore, the novel metabolic pathways led overall to metabolic inactivation, as concerns the estrogenic activity of nonylphenol through the ER.
Modulation of brassinosteroid-regulated gene expression by jumonji domain-containing proteins ELF6 and REF6 in <i>Arabidopsis</i> (2008)

Plant steroid hormones, brassinosteroids (BRs), are of great importance for plant growth and development. BRs signal through a cell surface receptor kinase, BRI1, and a GSK3-like kinase, BIN2, to regulate the BES1/BZR1 family of transcription factors, which directly bind to target gene promoters to activate or repress gene expression and mediate BR responses. To understand how BES1 regulates target gene expression, we identified two BES1-interacting proteins, ELF6 (early flowering 6) and its homolog REF6 (relative of early flowering 6), both of which are Jumonji N/C (JmjN/C) domain-containing proteins and were previously found to regulate flowering time. The interactions between BES1 and ELF6/REF6 were confirmed by GST pull-down and BiFC (bimolecular fluorescence complementation) experiments. Mutations in ELF6 or REF6 genes in Arabidopsis lead to BR-related phenotypes, including impaired cell elongation and reduced expression of BR target genes. Chromatin immunoprecipitation (ChIP) experiments indicated that histone 3 lysine 9 (H3K9) methylation status was changed in elf6 and ref6 mutants, consistent with recent findings that many Jmj proteins are histone demethylases. Our results demonstrate that BES1 recruits other transcriptional regulators such as ELF6 and REF6 to regulate target gene expression and coordinate BR responses with other developmental processes such as control of flowering time. Jmj domain-containing histone demethylases are involved in gene expression in many developmental processes and diseases, but how these proteins affect specific pathways is not well understood. Thus, our study establishes an important mechanism by which Jmj domain proteins modulate specific gene expression by interacting with pathway-specific transcription factors such as BES1.
Intraoperative brain shift prediction using a 3D inhomogeneous patient-specific finite element model (2007)

A set of algorithms for developing 3D patient-specific FE brain models is presented. Gravity-induced brain shift can be predicted using this model and displayed on high-resolution MR images. This strategy can be used not only for updating intraoperative MR imaging, but also for presurgical planning.
Route-Based Control of Hybrid Electric Vehicles (2008)

<div class="htmlview paragraph">Today's hybrid electric vehicle (HEV) controls do not necessarily provide maximum fuel savings over all drive cycles. An approach that employs route-based control could improve HEV efficiency at potentially minimal additional cost. This paper evaluates a range of route-based control approaches and identifies look-ahead strategies (using input from “on-the-fly” route predictions) as an area meriting further analysis. A novel implementation approach is developed and discussed, and a comparison with simulation results using an optimized general control setting indicates that fuel savings of approximately 2% to 4% can be obtained with route-based control. Given the increasing prevalence of GPS systems in vehicles, this advance has the potential to provide considerable aggregate fuel savings if applied across the entire national fleet. For instance, a 3% across-the-board reduction in HEV fuel use would save nearly 6.5 million gallons of fuel annually in the United States. These estimated savings will increase further as HEVs achieve greater market penetration.</div>
Cinnamate metabolism in ripening fruit : characterization of a UDP-glucose ; cinnamate glucosyltransferase from strawberry (2006)

Strawberry (Fragaria x ananassa) fruit accumulate (hydroxy)cinnamoyl glucose (Glc) esters, which may serve as the biogenetic precursors of diverse secondary metabolites, such as the flavor constituents methyl cinnamate and ethyl cinnamate. Here, we report on the isolation of a cDNA encoding a UDP-Glc:cinnamate glucosyltransferase (Fragaria x ananassa glucosyltransferase 2 [FaGT2]) from ripe strawberry cv Elsanta that catalyzes the formation of 1-O-acyl-Glc esters of cinnamic acid, benzoic acid, and their derivatives in vitro. Quantitative real-time PCR analysis indicated that FaGT2 transcripts accumulate to high levels during strawberry fruit ripening and to lower levels in flowers. The levels in fruits positively correlated with the in planta concentration of cinnamoyl, p-coumaroyl, and caffeoyl Glc. In the leaf, high amounts of Glc esters were detected, but FaGT2 mRNA was not observed. The expression of FaGT2 is negatively regulated by auxin, induced by oxidative stress, and by hydroxycinnamic acids. Although FaGT2 glucosylates a number of aromatic acids in vitro, quantitative analysis in transgenic lines containing an antisense construct of FaGT2 under the control of the constitutive 35S cauliflower mosaic virus promoter demonstrated that the enzyme is only involved in the formation of cinnamoyl Glc and p-coumaroyl Glc during ripening.
Topology-aware load balancing for performance portability over parallel high performance systems (2014)

This thesis presents our research to provide performance portability and scalability to complex scientific applications running over hierarchical multicore parallel platforms. Performance portability is said to be attained when a low core idleness is achieved while mapping a given application to different platforms, and can be affected by performance problems such as load imbalance and costly communications, and overheads coming from the task mapping algorithm. Load imbalance is a result of irregular and dynamic load behaviors, where the amount of work to be processed varies depending on the task and the step of the simulation. Meanwhile, costly communications are caused by a task distribution that does not take into account the different communication times present in a hierarchical platform. This includes nonuniform and asymmetric communication costs at memory and network levels. Lastly, task mapping overheads come from the execution time of the task mapping algorithm trying to mitigate load imbalance and costly communications, and from the migration of tasks. Our approach to achieve the goal of performance portability is based on the hypothesis that precise machine topology information can help task mapping algorithms in their decisions. In this context, we proposed a generic machine topology model of parallel platforms composed of one or more multicore compute nodes. It includes profiled latencies and bandwidths at memory and network levels, and highlights asymmetries and nonuniformity at both levels. This information is employed by our three proposed topology-aware load balancing algorithms, named NUCOLB, HWTOPOLB, and HIERARCHICALLB. Besides topology information, these algorithms also employ application information gathered during runtime. NUCOLB focuses on the nonuniform aspects of parallel platforms, while HWTOPOLB considers the whole hierarchy in its decisions, and HIERARCHICALLB combines these algorithms hierarchically to reduce its task mapping overhead. These algorithms seek to mitigate load imbalance and costly communications while averting task migration overheads. Experimental results with the proposed load balancers over different platform composed of one or more multicore compute nodes showed performance improvements over state of the art load balancing algorithms: NUCOLB presented improvements of up to 19% on one compute node; HWTOPOLB experienced performance improvements of 19% on average; and HIERARCHICALLB outperformed HWTOPOLB by 22% on average on parallel platforms with ten or more compute nodes. These results were achieved by equalizing work among the available resources, reducing the communication costs experienced by applications, and by keeping load balancing overheads low. In this sense, our load balancing algorithms provide performance portability to scientific applications while being independent from application and system architecture.
A Novel, Non-High-Dilution Method for Preparation of 1,1,2,2,9,9,10,10-Octafluoro[2.2]paracyclophane (2000)

A novel synthesis of octafluoro[2.2]paracyclophane (AF4), one that remarkably does not require the use of high dilution methodology, is presented. Using this unprecedented methodology, AF4 is produced in 60% yield in a reaction of Zn with 0.35 M p-bis(chlorodifluoromethyl)benzene in DMA at 100 degrees C. The process comprises a convenient, inexpensive, and highly scaleable preparation of AF4 for both research and commercial purposes.
Repaglinide, a new oral antidiabetic agent: a review of recent preclinical studies (1999)

Repaglinide is a new carbamoylmethyl benzoic acid derivative that is structurally related to meglitinide. In common with all active oral hypoglycaemic agents, it displays a comparable U-shaped configuration. Repaglinide exerts its effects by binding to a site on the plasma membrane of beta-cells, thereby closing ATP-sensitive potassium channels. This causes depolarization of the beta-cell and the opening of voltage-sensitive calcium channels allowing the influx of extracellular calcium ions. This increase in intracellular calcium, in turn, stimulates insulin release. The insulinotropic effect of repaglinide is not related to its ionophoretic capacity. Repaglinide does not cause insulin release in the absence of exogenous glucose, nor does it inhibit the biosynthesis of proinsulin. In vivo administration of an ester of succinic acid potentiates the insulin secretory response to concomitantly administered repaglinide. Repaglinide causes a more rapid increase in plasma insulin levels in rats than either glibenclamide or glimepiride.
Flat panel CT detectors for sub-second volumetric scanning (2005)

This paper explores the potential of flat panel detectors in sub-second CT scanning applications. Using a PaxScan 4030CB with 600um thick CsI(Tl), a central section of the panel (16 to 32 rows), was scanned at frame rates up to 1000fps. Using this platform, fundamental issues related to high speed scanning were characterized. The offset drift of the imager over 60 seconds was found to be less than 0.014 ppm/sec relative to full scale. The gain stability over a 10 hour period is better than +/- .45%, which is at the resolution limit of the measurement. Two different types of lag measurements were performed in order to separate the photodiode array lag from the CsI afterglow. The panel lag was found to be 0.41% 1<sup>st</sup> frame and 0.054% 25<sup>th</sup> frame at 1000fps. The CsI(Tl) afterglow, however, is roughly an order of magnitude higher, dominating the lag for sub-second scans. At 1000fps the 1<sup>st</sup> frame lag due to afterglow was 3.3% and the 25<sup>th</sup> frame lag was 0.34%. Both the lag and afterglow are independent of signal level and each follows a simple power law evolution versus time. Reconstructions of anatomical phantoms and the CATPHAN 500 phantom are presented. With a 2 second, 1200 projection scan of the CATPHAN phantom at 600fps in 32 slice mode, using 120kVp and CTDI<sub>100</sub> of 43.2mGy, 0.3% contrast resolution for a 6mm diameter target, can be visualized. In addition, 15lp/cm spatial resolution was achieved with a 2mm slice and a central CTDI<sub>100</sub> of 10.8mGy.
Sieve: cryptographically enforced access control for user data in untrusted clouds (2016)

Modern web services rob users of low-level control over cloud storage--a user's single logical data set is scattered across multiple storage silos whose access controls are set by web services, not users. The consequence is that users lack the ultimate authority to determine how their data is shared with other web services.

In this paper, we introduce Sieve, a new platform which selectively (and securely) exposes user data to web services. Sieve has a user-centric storage model: each user uploads encrypted data to a single cloud store, and by default, only the user knows the decryption keys. Given this storage model, Sieve defines an infrastructure to support rich, legacy web applications. Using attribute-based encryption, Sieve allows users to define intuitively understandable access policies that are cryptographically enforceable. Using key homomorphism, Sieve can reencrypt user data on storage providers in situ, revoking decryption keys from web services without revealing new keys to the storage provider. Using secret sharing and two-factor authentication, Sieve protects cryptographic secrets against the loss of user devices like smartphones and laptops. The result is that users can enjoy rich, legacy web applications, while benefiting from cryptographically strong controls over which data a web service can access.
Study of Electric System Harmonic Response (2004)

Frequency scanning is the simplest and most commonly used technique for harmonic analysis. It determines the system harmonic response at a node from the calculation of its impedance matrix. This paper studies the determination of these impedance matrices and presents a classification of such matrices according to the linear and nonlinear loads connected in the system. Finally, the results are applied to analyze the harmonic response of electric power systems in the presence of capacitor banks or Steinmetz systems. The analytical results obtained in the capacitor bank example have been validated with experimental measurements.
Effects of cholinesterase inhibition in supraspinal and spinal neural pathways on the micturition reflex in rats (2009)

These results indicate that activation of muscarinic cholinergic mechanisms by the cholinesterase inhibitor in the brain and spinal cord can inhibit the micturition reflex, mainly by affecting afferent pathways. These mAChR-induced inhibitory effects seem to be mediated through M(1)/M(3) receptor subtypes in the brain, while in the spinal cord, the M(1)/M(2) receptor subtypes might be involved in inhibitory effects, which are mediated via inhibition of mechanoceptive C-fibre afferent pathways.