gebhart/patrepeval huggingface dataset:
A Three-Phase Compressible Dual-Porosity Model for Streamline Simulation (2006)

Abstract Streamline methods as a reservoir simulation tool have generated a great deal of interest in petroleum engineering because of the capability to calculate fluid flow in multi-million cell geological models with reasonable CPU times. Recently, streamline simulation has been applied to fractured reservoirs at the geo-scale. However, these simulations have been limited to two-phase incompressible systems. Commercial application of streamline methods to fractured reservoirs often requires the modeling of at least three compressible fluid phases. Flow simulation of fractured reservoirs is commonly performed using a dual porosity model. The dual porosity system is modeled by using two coupled grids: one for matrix and one for fracture. The interaction between the two continua is modeled using matrix-fracture transfer functions. Until now, there were no mathematical models of dual porosity three-phase compressible flow for streamline simulators. To realize this model it was necessary to reformulate the matrix and fracture pressure equations. Conventional transfer function has been incorporated as a source/sink term, not only in the streamline saturation equations (as it was in incompressible case), but also in the pressure equation. The dual porosity model has been implemented into a streamline simulator. This tool has its main application in the high resolution reservoir modeling domain for analyzing geological uncertainty, model ranking and screening, and dynamic model calibration using production data. This paper describes the mathematical model for three-phase compressible dual porosity model for a streamline simulator and compares the results and run times of the streamline-based approach with a conventional dual porosity grid-based commercial simulator. The results from the streamline simulator for dual porosity show good agreement with those produced by a commercial finite difference simulator with order of magnitude improvement in simulation time.
Can structural MRI indices of cerebral integrity track cognitive trends in executive control function during normal maturation and adulthood? (2008)

We explored the relationship between structural neuroimaging-based indices of cerebral integrity and executive control function (ECF) in two groups of healthy subjects: A maturing group (33 subjects; 19-29 years) and a senescing group (38 adults; 30-90 years). ECF was assessed using the Executive Interview (EXIT) battery. Cortical indices of cerebral integrity included GM thickness, intergyral span, and sulcal span, each measured for five cortical regions per hemisphere. Subcortical indices included fractional anisotropy (FA), measured using track-based-spatial-statistics (TBSS), and the volume of T2-hyperintense WM (HWM). In the maturing group, no significant relationships between neuroanatomical changes and ECF were found; however, there were hints that late-term maturation of cerebral WM influenced variability in ECF. In the senescing group, the decline in ECF corresponded to atrophic changes in cerebral WM (sulcal and intergyral span) primarily in the superior frontal and anterior cingulate regions. A large fraction of the variability in ECF (62%) can be explained by variability in the structural indices from these two regions.
Joint Demand Response and Energy Trading for Electric Vehicles in Off-Grid System (2020)

This paper proposes a joint demand response and energy trading for electric vehicles in an off-grid system. We consider isolated microgrid in a region where, at a given time, some renewable energy generators have superflous energy for sale or to keep in storage facilities, whereas some electric vehicles wish to buy additional energy to meet their deficiency. In our system model, broker lead the market by determining the optimal transaction price by considering a trade-off between commission revenue and power reliability. Buyers and sellers follow the broker's decision by independently submitting a transaction price to the broker. Correspondingly transaction energy is allocated to the buyers in the proportion to their payment, whereas the revenue is allocated to the sellers in proportion to their sales. We investigated the economic benefits of such a joint demand response and energy trading by analyzing its hierarchical decision-making scheme as a single-leader-heterogeneous multi-follower Stackelberg game. With demonstrating an existence of a unique Stackelberg equilibrium, we show that the transaction price in the proposed market model is up to 25.8% cheaper than the existing power market. In addition, we compare the power reliability results with other algorithm to show the suitability of proposed algorithm in the isolated microgrid environment.
Energiamurroksen ennakoidut vaikutukset 2030: Lämpöpumput, aurinkolämpö ja lämmön varastointi (2016)

Tämä case-julkaisu liittyy Suomen Akatemian strategisen tutkimuksen neuvoston rahoittamaan Smart Energy Transition (SET) -hankkeeseen (293405) (www.smartenergytransition.fi). SET-hanke tutkii, miten Suomi voi hyötyä hajautetun ja vaihtelevan uusiutuvan energian ympärille nousevista murroksellisista teknologioista. Kyse on ratkaisuista, joissa energiaa voidaan varastoida tai sen tarvetta ohjata vaihtelevan tuotannon mukaan (kysyntäjousto). Näihin ratkaisuihin liittyvät olennaisesti uudet digitaaliset ratkaisut, kuten esineiden internet. Samalla murrokseen liittyy myös kehitys, jossa rakennusten ja liikenteen energian tarve pienenee, energiaomavaraisuus kasvaa, ja rakennukset ja liikennevälineet muodostavat yhä kiinteämmän osan energiajärjestelmää.
Tau pathology vulnerable neuronal subpopulation in Alzheimer’s disease (2022)

Abstract Background Tau pathology is known as a primary driver of neurodegeneration in Alzheimer’s disease (AD). Understanding its underlying molecular mechanism is critical in expanding our knowledge of AD pathogenesis and developing novel AD therapeutic strategies. However, interrogating tau induced neurotoxicity mechanisms has been difficult due to heterogeneous susceptibility of neurons to tau pathology. Here, we aim to identify the most vulnerable neuronal subpopulation to tau pathology in AD and reveal more clear molecular mechanisms of tau induced neuro‐toxicity/degeneration by analyzing gene expression changes in the vulnerable population. Method We performed single nuclei RNA sequencing and tau biochemistry from same tissue blocks of the same AD patients (5 brain regions of 32 AD donors with various Braak stages). About 1.5x10 6 neurons were enriched in total by NeuN antibody‐based flow cytometry sorting and these cells were clustered into 15 neuronal subpopulations based on their similarity in gene expression. We tested for association between relative neuronal population abundance and tau pathology readouts (phospho‐T231 ELISA, HT7‐HT7 SIMOA and HEK seeding). Based on the strength of correlation, we identified the neuronal subpopulation that reduces relative abundance in association with its tau pathology. Result We identified a tau vulnerable neuronal population that showed strong negative correlation between its relative abundance and tau pathology readouts in BA20 and BA46. The population was one of largest excitatory subpopulation distinguished by marker genes, CBLN2 and LINC00507. This outcome was supported by multiple published transcriptomics studies and histologically validated by multiplexed in situ hybridization and immunohistochemistry. Differential gene expression analysis of the vulnerable neuronal population identified a list of genes that potentially links tau pathology and neuronal death. Conclusion This study with large number of captured neurons for single cell transcriptomics and quantitative tau pathology readout for direct comparison to transcriptomics data enabled the discovery of a vulnerable neuronal subpopulation in more precise manner and revealed genes related to tau associated neurotoxicity more clearly. This result serves as a great starting point to further interrogate fundamental mechanisms of tau‐driven neurodegeneration in AD and accelerate therapeutic target and biomarker discovery.
HIV vaccines: The myth of cross-reactive T cells (2003)

The variability of HIV has raised the question of whether T cells raised against one strain can cross-react with another. This is highly pertinent to vaccine design, especially as most vaccines being prepared are B clade and more than 90% of infections worldwide are non-B clade. The clades differ by more than 20% in amino acid sequence. The idea that virus-specific T cells are cross-reactive goes back to a misconception in the 1970s and 1980s when it was found by us and others that cytotoxic T lymphocytes could not distinguish between influenza viruses of the different A virus subtypes. It was assumed that CTLs recognized virus glycoproteins which differ by 30% between subtypes so they must be permissive in antigen recognition. Later work by us and others showed that these T cells recognized the highly conserved internal virus proteins, which are processed within the cell before presentation by MHC class I molecules at the cell surface. Thus virus-specific T cells were not widely cross-reactive, but the idea was firmly rooted and still persists. HIV is the most variable virus known to infect humans. Besides the clade differences there are quasispecies swarms within each patient with 4-10% variation. We and others have shown that HIV can escape CTL responses by point mutations and recent data indicate that this is commonplace. This alone suggests that T cells are sensitive to mutations in the epitopes. However (nearly) all the mutations that have been shown to be selected by T-cell pressure contain mutations in the residues that anchor the peptide to the HLA molecule. Thus there was still space for T cells that cross-react broadly on epitopes that bind. To test this, we made all 171 single amino acid changes in the immunodominant epitope in HIV gag presented by HLA-A2 in more than 70% of HLA-A2 positive patients: SLFNTVATL. Using two clones with completely different T-cell receptors that were already known to be cross-reactive between the common F3Y variants we found that more than two thirds of the altered peptides were not recognized and that most of these changes occurred in side chains involved in TCR recognition. Side chains were orientated by crystallizing SLFNTVATL + HLA-A2. When the common F3Y variant was crystallized however, it showed a 180-degree rotation in the central region of the peptide. Further analysis of recognition of amino acids changed in these positions indicated that one conformation is seen and the TCR probably triggers a rotation in the peptide so that both variants look identical. Thus the TCRs that recognize this peptide are extremely sensitive to amino acid changes in TCR interaction regions. Given that virus-specific T cells are often oligoclonal, this form of escape may be common. The sensitivity of CTLs to peptide variation makes escape relatively easy for HIV. For the same reasons, tumors may also easily escape T-cell recognition. This abstract was published in Cancer Immunity , a Cancer Research Institute journal that ceased publication in 2013 and is now provided online in association with Cancer Immunology Research .
Target enzymes for plasma proteinase inhibitors. (1986)

The control of proteolytic activity in tissues is primarily under the influence of plasma inhibitors which function to rapidly inactivate specific target proteinases by either covalent interactions or trapping reactions. Each inhibitor is designed to control a specific proteolytic event, although many may show weaker activities against other proteinases. Kinetic experiments, however, indicate that reactions with target enzymes are much more rapid than with other and that modification of the inhibitor dramatically interferes with the rate at which inhibition occurs. This latter effect is almost certainly due to the fact that the inhibitor itself acts as a perfect substrate for the proteinase in question, resulting in a rapid association with the enzyme followed by a very slow dissociation so that the enzyme is essentially trapped in a complex.
The Role of Context Selection in Object Detection (2016)

We investigate the reasons why context in object detection has limited utility by isolating and evaluating the predictive power of different context cues under ideal conditions in which context provided by an oracle. Based on this study, we propose a region-based context re-scoring method with dynamic context selection to remove noise and emphasize informative context. We introduce latent indicator variables to select (or ignore) potential contextual regions, and learn the selection strategy with latent-SVM. We conduct experiments to evaluate the performance of the proposed context selection method on the SUN RGB-D dataset. The method achieves a significant improvement in terms of mean average precision (mAP), compared with both appearance based detectors and a conventional context model without the selection scheme.
Optimal multiple-impulse satellite evasive maneuvers (1994)

Minimum-fuel, impulsive solutions are obtained for the evasive maneuver of a satellite followed by a rendezvous with the original orbit station. The evasion distance and time are constrained. Both free and constrained final time cases are considered. Primer vector theory is used to obtain optimal solutions, which include threeimpulse solutions for an arbitrarily oriented evasion radius vector of a specified magnitude, and two-impulse free-return trajectories for certain specific evasion radius vectors. On some three-impulse solutions the primer vector indicates that the addition of a fourth impulse to the return trajectory will lower the fuel cost. Nomenclature A =3X3 coefficient matrix in CW equations, Eq. (2) B =3X3 coefficient matrix in CW equations, Eq. (3) D = determinant of the matrix N, Eq. (A6) H = Hamiltonian function, Eq. (B9) / = velocity-change cost of nominal three-impulse trajectory K = time interval between initial and midcourse impulse, tm ~ t0
RedH and PigC Catalyze the Biosynthesis of Hybrubins via Phosphorylation of 4′-Methoxy-2,2′-Bipyrrole-5′-Carbaldehyde (2019)

Hybrubins are "unnatural" alkaloids with the same 4'-methoxy-2,2'-bipyrrole-5'-methine moiety found in prodiginines and a different ring derived from tetramic acids. Here, we demonstrated that RedH, a homologue of prodigiosin synthetase PigC, was responsible for the biosynthesis of hybrubins A and B in <i>Streptomyces lividans</i><i>In vitro</i> reactions indicated that RedH and PigC catalyzed the intermolecular condensation between 4'-methoxy-2,2'-bipyrrole-5'-carbaldehyde (MBC) and (<i>Z</i>)-5-ethylidenetetramic acid (ETA) to produce hybrubin B. Moreover, we demonstrated that RedH and PigC activated MBC via phosphorylation of the aldehyde group to form an intermediate P<sub>i</sub>-MBC and that the subsequent condensation between P<sub>i</sub>-MBC and (<i>Z</i>)-5-ethylidenetetramic acid occurs in a nonenzymatic way.<b>IMPORTANCE</b> Hybrubins are an emerging class of prodiginines possessing a new C ring derived from 5'-substituted tetramic acids and the methylene bridge connecting the C ring at a different position. We have supposed that condensation between 4'-methoxy-2,2'-bipyrrole-5'-carbaldehyde (MBC) and 5-ethylidenetetramic acid (ETA) yields the hybrid natural products hybrubins, which was proposed to be catalyzed by the undecylprodigiosin synthetase RedH. However, it is doubted whether RedH is able to catalyze another type of condensation between MBC and tetramic acids. In this study, we have demonstrated that the MBC-ETA condensation proceeds through RedH/PigC-catalyzed enzymatic activation of MBC via phosphorylation and a nonenzymatic condensation of P<sub>i</sub>-MBC with ETA. Since MBC analogues have been shown to be accepted by PigC, more hybrubin analogues might be produced by using combinations of MBC analogues and other tetramic acids in future studies.
Supplementary Movies 4-6 from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma (2023)

&lt;p&gt;In vitro killing assay movies. Co-culture of 12T melanoma cells with irrelevant 108TILs&lt;/p&gt;
A Pulse-Current Implementation Using Phase-Shift Modulation in Smart Battery (2020)

Pulsed current provides a rest-time for battery cells to fully complete internal chemical reactions that can suppress the increase of resistance to extend the battery lifetime. This paper proposes a new method to implement pulsed current using synchronized/unsynchronized Phase-Shift Modulation during both charging and discharging processes in a smart battery management system. Faulty cells can be permanently bypassed without any impact on the architecture of the Smart Battery. Simulation and experimental results verify the feasibility of the proposed method.
Messraten statischer Einzelspiegel-Fourier-Transformations-Infrarotspektrometer bei Verwendung von Mikrobolometerdetektoren (2017)

Zusammenfassung Statische Einzelspiegel-Fourier-Transformations-Spektrometer ermöglichen Spektroskopie mit hohen Messraten im mittleren infraroten Spektralbereich, da sie geringe interne Lichtverluste aufweisen und gleichzeitig auf bewegliche Teile vollständig verzichten. In dieser Arbeit wird ein solches Spektrometer vorgestellt, optimiert und auf seine maximale Messrate hin untersucht. Ausgestattet mit einem ungekühlten Mikrobolometerarray als Detektor erlaubt es Bildwiederholraten bis 200 Hz bei einer Auflösung von 7.1 cm – 1 im Spektralbereich zwischen 1250 cm – 1 und 650 cm – 1 . Durch die hohe thermische Zeitkonstante des Mikrobolometerarrays ist für quantitative spektrale Messungen die Messrate des Gesamtsystems auf 15 Hz zu reduzieren.
Oleic acid regulates hippocampal neurogenesis as a TLX ligand (2022)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Analysis of circadian properties and healthy levels of blue light from smartphones at night (2015)

This study proposes representative figures of merit for circadian and vision performance for healthy and efficient use of smartphone displays. The recently developed figures of merit for circadian luminous efficacy of radiation (CER) and circadian illuminance (CIL) related to human health and circadian rhythm were measured to compare three kinds of commercial smartphone displays. The CIL values for social network service (SNS) messenger screens from all three displays were higher than 41.3 biolux (blx) in a dark room at night, and the highest CIL value reached 50.9 blx. These CIL values corresponded to melatonin suppression values (MSVs) of 7.3% and 11.4%, respectively. Moreover, smartphone use in a bright room at night had much higher CIL and MSV values (58.7 ~ 105.2 blx and 15.4 ~ 36.1%, respectively). This study also analyzed the nonvisual and visual optical properties of the three smartphone displays while varying the distance between the screen and eye and controlling the brightness setting. Finally, a method to possibly attenuate the unhealthy effects of smartphone displays was proposed and investigated by decreasing the emitting wavelength of blue LEDs in a smartphone LCD backlight and subsequently reducing the circadian effect of the display.
Thin-film filters with diffractive and waveguiding layers (1996)

By merging traditional thin-film optics with diffractive and waveguide optics, it has been shown theoretically that optical reflection filters can be designed with 100% efficiency, symmetrical lineshapes, near-zero nonoscillatory sidebands over extended wavelength regions, narrow (or wide) controllable linewidths, and other favorable attributes [1]. Thus, single- and multilayer reflective filters with near ideal features have been theoretically demonstrated by utilizing anti-reflection design to suppress reflections adjacent to the resonance peak [2]. In addition, a transmission bandpass filter can be designed using guided-mode resonance effects with a highly reflecting dielectric multilayer stack [3]. This new transmission filter produces broad-range low-transmission sidebands with nearly 100% transmission efficiency at the passband. Numerous applications have been identified including laser resonator frequency-selective polarizing mirrors, laser cavity tuning elements, mirrors and phase-locking elements for vertical-cavity surface emitting laser arrays, and sensor elements [4]. Experimental results verifying the theoretically predicted high resonance efficiencies for reflection filters have been reported in the optical spectral region [5,6], in the millimeter wave region [7], and in the microwave region [8].
Magnetite Nanoparticles for Magnetic Fluid Hyperthermia Using Modified Oxidation Method (2007)

Magnetic fluid hyperthermia (MFH) utilizing the heat generated by the magnetic particles exposed to external AC magnetic field has an edge over the other hyperthermia techniques, since the heat source can be localized in cancer cells with an external magnetic field and their position can be detected by utilizing their magnetic properties. Heating rate depends on the particle diameters and the experimental investigations by using magnetite particles suggested that the optimal size could be above 11nm. Thus, in this paper, a technique to synthesize monodispersed magnetite particles with diameters raging between 11 and 20 nm is reported. Furthermore, a detailed analysis of the relationship between particle size and heating rate is reported based on the magnetic and heat dissipation properties of magnetite particles synthesized by the modified oxidation method.
Conservative-Bayesian Mechanisms (2010)

We put forward a new class of mechanisms. In this extended abstract, we exemplify our approach only for single-good auctions in what we call a conservative-Bayesian setting. (Essentially, no common-knowledge about the underlying distribution of the players' valuations is required.) We prove that our mechanism is optimal in this challenging and realistic setting.
Gender-dependent effect of Gpbar1 genetic deletion on the metabolic profiles of diet-induced obese mice (2010)

G-protein-coupled bile acid receptor 1 (GPBAR1/TGR5/M-Bar/GPR131) is a cell surface receptor involved in the regulation of bile acid metabolism. We have previously shown that Gpbar1-null mice are resistant to cholesterol gallstone disease when fed a lithogenic diet. Other published studies have suggested that Gpbar1 is involved in both energy homeostasis and glucose homeostasis. Here, we examine the functional role of Gpbar1 in diet-induced obese mice. We found that body weight, food intake, and fasted blood glucose levels were similar between Gpbar1-null mice and their wild-type (WT) littermates when fed a chow or high-fat diet (HFD) for 2 months. However, insulin tolerance tests revealed improved insulin sensitivity in male Gpbar1(-/-) mice fed chow, but impaired insulin sensitivity when fed a HFD. In contrast, female Gpbar1(-/-) mice exhibited improved insulin sensitivity when fed a HFD compared with their WT littermates. Female Gpbar1(-/-) mice had significantly lower plasma cholesterol and triglyceride levels than their WT littermates on both diets. Male Gpbar1(-/-) mice on HFD displayed increased hepatic steatosis when compared with Gpbar1(+)(/)(+) males and Gpbar1(-/-) females on HFD. These results suggest a gender-dependent regulation of Gpbar1 function in metabolic disease.
Time-to-Breakdown Behavior and Mechanism on U-grooved n-MOSFET (2009)

The bi-modal breakdown processes can well explain the lifetime model in grooved gate oxide with rounded local structure. We have clarified for the first time that the gate oxide reliability is strongly dependant on the tunneling characteristics in the rounded channel of the center and the N+ junction edge corners