gebhart/patrepeval huggingface dataset:
Localization of Phospholipase D1 to Caveolin-enriched Membrane via Palmitoylation: Implications for Epidermal Growth Factor Signaling (2002)

Phospholipase D (PLD) has been suggested to mediate epidermal growth factor (EGF) signaling. However, the molecular mechanism of EGF-induced PLD activation has not yet been elucidated. We investigated the importance of the phosphorylation and compartmentalization of PLD1 in EGF signaling. EGF treatment of COS-7 cells transiently expressing PLD1 stimulated PLD1 activity and induced PLD1 phosphorylation. The EGF-induced phosphorylation of threonine147 was completely blocked and the activity of PLD1 attenuated by point mutations (S2A/T147A/S561A) of PLD1 phosphorylation sites. The expression of a dominant negative PKCalpha mutant by adenovirus-mediated gene transfer greatly inhibited the phosphorylation and activation of PLD1 induced by EGF in PLD1-transfected COS-7 cells. EGF-induced PLD1 phosphorylation occurred primarily in the caveolin-enriched membrane (CEM) fraction, and the kinetics of PLD1 phosphorylation in the CEM were strongly correlated with PLD1 phosphorylation in the total membrane. Interestingly, EGF-induced PLD1 phosphorylation and activation and the coimmunoprecipitation of PLD1 with caveolin-1 and the EGF receptor in the CEM were significantly attenuated in the palmitoylation-deficient C240S/C241S mutant, which did not localize to the CEM. Immunocytochemical analysis revealed that wild-type PLD1 colocalized with caveolin-1 and the EGF receptor and that phosphorylated PLD1 was localized exclusively in the plasma membrane, although some PLD1 was also detected in vesicular structures. Transfection of wild-type PLD1 but not of C240S/C241S mutant increased EGF-induced raf-1 translocation to the CEM and ERK phosphorylation. This study shows, for the first time, that EGF-induced PLD1 phosphorylation and activation occur in the CEM and that the correct localization of PLD1 to the CEM via palmitoylation is critical for EGF signaling.
Cascaded Models for Better Fine-Grained Named Entity Recognition (2020)

Named Entity Recognition (NER) is an essential precursor task for many natural language applications, such as relation extraction or event extraction. Much of the NER research has been done on datasets with few classes of entity types (e.g. PER, LOC, ORG, MISC), but many real world applications (disaster relief, complex event extraction, law enforcement) can benefit from a larger NER typeset. More recently, datasets were created that have hundreds to thousands of types of entities, sparking new lines of research (Sekine, 2008;Ling and Weld, 2012; Gillick et al., 2014; Choiet al., 2018). In this paper we present a cascaded approach to labeling fine-grained NER, applying to a newly released fine-grained NER dataset that was used in the TAC KBP 2019 evaluation (Ji et al., 2019), inspired by the fact that training data is available for some of the coarse labels. Using a combination of transformer networks, we show that performance can be improved by about 20 F1 absolute, as compared with the straightforward model built on the full fine-grained types, and show that, surprisingly, using course-labeled data in three languages leads to an improvement in the English data.
Prolonged transposed polynomial-based filters for decimation (2003)

If sample rate conversion (SRC) is performed between arbitrary sample rates, then the SRC factor can be a ratio of two very large integers or even an irrational number. An efficient way to reduce the implementation complexity of a SRC system in those cases is to use polynomial-based interpolation filters. The impulse response of these filters is of a finite duration and piecewise polynomial so that it is expressible in each subinterval of the same length T by means of a polynomial of a low order. Here, T can be equal to, a multiple of, or a fraction of either the input or output sample period. The actual implementation of the polynomial-based filters can be performed directly in the digital domain effectively by using the Farrow structure or its modifications. This paper introduces for an arbitrary sampling rate reduction a novel implementation form referred to as the prolonged transposed modified Farrow structure. For this structure, T is an integer multiple of the output sampling period. Compared with the modified transposed Farrow structure, it has a narrowed pass-band region with almost the same complexity. In addition, a decimator structure consisting of a cascade of the prolonged transposed Farrow structure and a fixed linear-phase finite-impulse response decimator is introduced in order to reduce the overall computational complexity.
A Generalized Process for Optimal Threshold Setting in HUMS (2007)

Monitoring the health of a helicopter drive train enhances flight safety and reduces operating costs. Health and usage management systems (HUMS) monitor the drive train by using accelerometers to measure component vibration. Algorithms process the time domain vibration data into various condition indicators (CI), which are used to determine component health via thresholding. For the rotating machinery, a standard set of CI are shaft order one, two and three (i.e. 1, 2 or 3 times the shaft RPM). Shaft order one (SOI) is indicative of an unbalance, where as higher shaft order can be used to detect a bent shaft or misalignment condition. In the case of bearings, CIs are envelope spectrum or cepstrum analysis of the ball, cage, inner race and outer race frequencies. There are a number of standard CI used for gear analysis, such as line elimination and resynthesis, side band modulation, gear misalignment, etc. In general, some method is used to set thresholds for these CIs: when the threshold is exceeded, maintenance is recommended. The HUMS system must balance the risk of setting the threshold too high such that a component may fail in flight versus the risk of setting the threshold too low, which results in additional maintenance cost. This paper covers a generalized process of optimally setting threshold for CI and fusing the information into an Health Indicator. It can be shown that the distributions of CI for shaft magnitude and bearing envelop energy are Rayleigh distribution. The normalized distance functions for these CIs are a Nakagami distribution with mu (shape parameter) of n (number of CI) and Omega (scale parameter) of 2 x 1/(2-pi/2) x mu. For gear CIs, which are considered as Gaussian, the normalized distance function is again Nakagami, but with a mu of nil and Omega of n. Given the theoretical mu and Omega, a threshold for any set of CI can be generated resulting in system probability of false alarm (PFA). This is an optimal decision rule for detecting a component which is no longer nominal. The normalized distance distribution is a function of the component CI sample statistic. Procedures are developed to calculate the unbiased statistic: covariance for Rayleigh based CIs and mean value/covariance for Gaussian based CIs. In the cases where the population of components is not nominal (e.g. mass imbalances which violate the Rayleigh assumption) tools are presented to control this. For gear, normalizing transforms can be used to ensure the CIs are more Gaussian. Example data from utility helicopters are given.
Bengal rose@dendritic box (1996)

Abstract Bengal Rose was succesfully encapsulated and liberated from a dendritic box. Bengal Rose@DAB‐ dendr ‐(NH‐ t ‐BOC‐L‐Phe) 64 was investigated with several different techniques such as ultraviolet, circular dichroism and fluorescence spectroscopy.
Air-Cooled Battery-Pack Thermals and Capacities Under Various Operating Temperatures and Processes (2020)

Battery packs can be used to provide emergency power during power outages to allow ride-through until restoration of backup power or alternatively, provide sufficient uptime to allow the system to backup or save data and records and enact a safe shutdown. Using battery packs also contributes to a more robust power design and higher immunity to power line disturbance. Thermal management of large battery packs remains a challenge due to complex heat transfer mechanisms and pathways. In this paper, we investigate the thermal profile within a battery pack during the critical charging and discharging process as well as the impact of operating environments on battery capacities. Thermocouples were installed on multiple batteries along the air flow stream as well as at several points on a single cell to investigate pack-level thermal management and heat distribution within a single cell respectively. Experiments found a large amount of heat was generated during the shorter discharging process compared to the longer battery charging process. Charge capacities of four air cooled battery packs were measured at various temperatures during the charging and discharging process and were found to be reduced at both lower and higher operating temperatures.
Surface-enhanced Raman scattering for the detection of polycystic ovary syndrome (2018)

Polycystic ovary syndrome (PCOS) is a multi-factorial heterogeneous syndrome that affects many women of reproductive age. This work demonstrates how the surface-enhanced Raman scattering (SERS) technique can be used to differentiate between PCOS and non-PCOS patients. We determine that the use of SERS, in conjunction with partial least squares (PLS) and principal component analysis (PCA), allows us to detect PCOS in patient samples. Although the role of chemerin in the pathogenesis of PCOS patients is not clear, this work enables us to measure their chemerin levels using the PLS regression method.
Development of Ecdysone-Regulated Lentiviral Vectors (2004)

We have engineered a lentivirus-based gene transfer system to achieve ecdysone-regulated transgene expression. The method combines the wide tropism of lentiviral vectors and the possibility of gene regulation by a small molecule with an excellent pharmacological profile. Using the hematopoietic tissue as a model, we transduced mouse progenitors with an ecdysone-regulated GFP expression cassette. The ecdysone gene switch efficiently turned GFP on and off in transplanted animals, showing low basal activity. This system allows the delivery of inducible transcriptional units in vitro and ex vivo and may be a useful tool for gene transfer purposes. Moreover, our work provides hints on the design of lentiviral vectors containing multiple expression cassettes with multiple promoters.
Goniometric motion controller for the superconducting coil in a magnetic stereotaxis system (1991)

For the purpose of positioning the 80 kg, 2 T superconducting coil/cryostat used in the developmental version of a magnetic stereotaxis system, a four degree-of-freedom goniometer has been designed, built, and tested. Computer-controlled, stepping motor actuators enable movement of the coil via either joystick, keyboard, or translator-module keypad commands. An integral arrangement of counterweights and counterbalances minimizes the overall weight and size of the goniometer, while maintaining static and dynamic stability during operation. As much of the structure as possible has been made of nonmagnetic materials (mostly aluminum) to minimize distortion of the superconducting coil's field. In this paper, we present the design principles for the goniometer, describe the essential features of its construction, and discuss its performance characteristics and limitations. We also discuss a strategy for performing precision magnetic stereotaxis procedures with an arrangement of static superconducting coils.
Metabolic evaluation and medical management of staghorn calculi (2019)

Staghorn renal calculi are large renal calculi that occupy nearly the entirety of the renal collecting system. They may be composed of metabolic or infection stone types. They are often associated with specific metabolic defects. Infection stones are associated with urease-producing bacterial urinary tract infections. The ideal treatment for staghorn calculi is maximal surgical removal. However, some patients are either unwilling or unable to proceed with that modality of treatment, and therefore other management must be used. One such technique is the metabolic evaluation with directed medical management. Based on contemporary evidence that the majority of staghorn stones are metabolic in etiology, and furthermore that even infection stones are usually associated with metabolic abnormalities, metabolic evaluation with directed medical management is recommended for all staghorn stone formers. The scientific basis of this recommendation is reviewed in the present work.
Micro-thermal-fluid transient analysis and active control for two-phase microelectronics cooling (2010)

Because of increasing power densities, microchannel systems are being explored for two-phase cooling of ultra high power electronic devices. Flow instability is a potential problem in any two-phase microchannel cooling system especially for transient applications. With various two-phase flow stabilities possible in a microscale boiling system, the overall cooling performance deteriorates significantly. For better dynamic thermal management of microelectronic systems, a family of oscillatory flow boiling heat transfer correlations and active stabilizing flow control methods have been developed.
Brentuximab vedotin for relapsed or refractory CD30+ hematologic malignancies: the German Hodgkin Study Group experience (2012)

The CD30-targeting Ab-drug conjugate brentuximab vedotin (SGN-35) was recently approved for the treatment of relapsed Hodgkin lymphoma and anaplastic large-cell lymphoma by the Food and Drug Administration. In the present study, we report the experience of the German Hodgkin Study Group with brentuximab vedotin as single agent in 45 patients with refractory or relapsed CD30(+) Hodgkin lymphoma who were treated either in a named patient program (n = 34) or in the context of a safety study associated with the registration program of this drug. In these very heavily pretreated patients, an objective response rate of 60%, including 22% complete remissions, could be documented. The median duration of response was 8 months. This retrospective analysis supports the previously reported excellent therapeutic efficacy of brentuximab vedotin in heavily pretreated CD30(+) malignancies.
Performance Analysis of OFDM with Wiener Phase Noise and Frequency Selective Fading Channel (2011)

We analyze the effect of Wiener phase noise on the capacity and signal-to-interference-plus-noise (SINR) ratio. Our analysis includes phase noise at the transmitter and receiver end of an OFDM communication link. We see that the capacity and SINR are random variables whose distribution depends on the phase noise and the fading channel. Using a Taylor series approximation, we show that the random variable, characterizing the phase noise, in the performance metrics can be expressed as a sum of correlated gamma variables with rank-deficient square-root normalized covariance matrix. The approximation holds well when the ratio between the subcarrier spacing and the 3dB bandwidth of the oscillator power spectral density is at least one order of magnitude, which for most practical oscillators is the case. In earlier literature, the probability density function of a sum of correlated gamma variables with full-rank square-root normalized covariance matrix was derived. We extend these results to the rank-deficient case and apply them to the random variable of our case. With the probability density functions characterizing the phase noise and the fading channel at hand, we proceed to obtain closed-form statistical measures of capacity and SINR. The simulations show the good agreement with our analytical expressions.
Supplementary Table 3 from Genome-wide Methylation Analysis Identifies Genes Specific to Breast Cancer Hormone Receptor Status and Risk of Recurrence (2023)

&lt;p&gt;XLS file - 32K&lt;/p&gt;
Malthusian Reinforcement Learning (2019)

Here we explore a new algorithmic framework for multi-agent reinforcement learning, called Malthusian reinforcement learning, which extends self-play to include fitness-linked population size dynamics that drive ongoing innovation. In Malthusian RL, increases in a subpopulation's average return drive subsequent increases in its size, just as Thomas Malthus argued in 1798 was the relationship between preindustrial income levels and population growth. Malthusian reinforcement learning harnesses the competitive pressures arising from growing and shrinking population size to drive agents to explore regions of state and policy spaces that they could not otherwise reach. Furthermore, in environments where there are potential gains from specialization and division of labor, we show that Malthusian reinforcement learning is better positioned to take advantage of such synergies than algorithms based on self-play.
How to Use Bitcoin to Play Decentralized Poker (2015)

Back and Bentov (arXiv 2014) and Andrychowicz et al. (Security and Privacy 2014) introduced techniques to perform secure multiparty computations on Bitcoin. Among other things, these works constructed lottery protocols that ensure that any party that aborts after learning the outcome pays a monetary penalty to all other parties. Following this, Andrychowicz et al. (Bitcoin Workshop 2014) and concurrently Bentov and Kumaresan (Crypto 2014) extended the solution to arbitrary secure function evaluation while guaranteeing fairness in the following sense: any party that aborts after learning the output pays a monetary penalty to all parties that did not learn the output. Andrychowicz et al. (Bitcoin Workshop 2014) also suggested extending to scenarios where parties receive a payoff according to the output of a secure function evaluation, and outlined a 2-party protocol for the same that in addition satisfies the notion of fairness described above. In this work, we formalize, generalize, and construct multiparty protocols for the primitive suggested by Andrychowicz et al. We call this primitive secure cash distribution with penalties. Our formulation of secure cash distribution with penalties poses it as a multistage reactive functionality (i.e., more general than secure function evaluation) that provides a way to securely implement smart contracts in a decentralized setting, and consequently suffices to capture a wide variety of stateful computations involving data and/or money, such as decentralized auctions, market, and games such as poker, etc. Our protocol realizing secure cash distribution with penalties works in a hybrid model where parties have access to a claim-or-refund transaction functionality FCR}* which can be efficiently realized in (a variant of) Bitcoin, and is otherwise independent of the Bitcoin ecosystem. We emphasize that our protocol is dropout-tolerant in the sense that any party that drops out during the protocol is forced to pay a monetary penalty to all other parties. Our formalization and construction generalize both secure computation with penalties of Bentov and Kumaresan (Crypto 2014), and secure lottery with penalties of Andrychowicz et al. (Security and Privacy 2014).
Managing Failures of Aircraft Systems by Coapplication of Parametric and Nonparametric Methods (2011)

Analysis of failures that occur in an actual operational environment is very important for the maintenance service providers and manufacturers to offer specific maintenance solutions or product improvements tailored to the customers’ needs and to survive in the highly competitive aviation market. There are mainly two methodologies for failure analysis: Parametric approach and nonparametric approach. Practitioners usually prefer one of these methodologies alone for monitoring or predicting the failure trends. However, each methodology has its own strengths and weaknesses for any application. Therefore, it may be useful to view these methods as being complementary for obtaining the most benefit from the failure analysis. This paper brings the parametric and nonparametric methodologies together for extracting valuable management information from the field failures of aircraft systems with an example of auxiliary power unit application. Opportunities of coapplication of the methodologies are described for identifying failure trends and unusual behaviors and revealing hidden information that may otherwise not be detected by the application of only one of those methodologies.
Identification of human endogenous retrovirus (HERV-K(HML-2))-specific mucosal CD4+ T cell responses in HIV-1-exposed, seronegative individuals (P6195) (2013)

Abstract The transcriptional silence of human endogenous retroviruses (HERV) can be disrupted in HIV-1 infection. We have reported that the strength of the HERV-specific CD8+ T cell response predicts lower HIV-1 viral load in untreated adults. To determine whether HERV-K immunity plays a role in inhibiting HIV-1 replication at a major site of transmission and CD4+ T cell depletion, we assessed these responses in gut-associated lymphoid tissue (GALT) from rectosigmoid biopsies and blood of HIV-1 exposed, seronegative (HESN) individuals (n=6) by flow cytometry. CMV pp65- and HIV-1 Gag-specific T cells were also measured, and all responses were compared with peripheral antigen-specific responses in uninfected, low-risk controls (n=11). With the exception of stronger CMV-specific CD8+ T cell responses in the HESN group (p=0.024), there were no significant differences between the magnitudes of peripheral antigen-specific T cell responses in the HESN vs. controls. However, HESN subjects had remarkably robust mucosal HIV-1- (median %CD4+cytokine+cells=2.67) and HERV-specific (median %CD4+cytokine+cells=3.41) CD4+ responses, which were much stronger than the corresponding PBMC responses (p=0.0079 and p&amp;lt;0.0001, respectively). These findings suggest that the GALT is an important site of HERV-K expression and immunity in individuals exposed to HIV-1, and should be further investigated in the context of novel vaccine strategies that target conserved antigens such as HERV.
Combined photodynamic therapy with systemic chemotherapy for unresectable cholangiocarcinoma (2019)

Combination photodynamic therapy and chemotherapy was well tolerated and resulted in significantly longer survival than chemotherapy alone. Application of photodynamic therapy significantly correlated with longer survival, demonstrating benefit in advanced cholangiocarcinoma. Thus, photodynamic therapy should be considered during therapeutic decision making in advanced cholangiocarcinoma.
Interference suppression in the presence of quantization errors (2009)

Multi-element antennas offer the possibility of increasing the spatial reuse of wireless spectrum by ¿nulling¿ out interfering signals. However, the interference suppression performance is highly sensitive to small errors in the gains applied to the antenna elements. In this paper, we examine in detail the effect of one specific source of error that arises from quantizing array weights. We show that a simple approach based on scalar quantization that ignores the correlation of the quantization errors fails to fully utilize the interference suppression capability of the array: the residual interference level does not decrease with the number of antennas. Unfortunately, the optimum approach to computing the weights involves vector quantization over a space that grows exponentially with the number of antennas and number of quantization bits, and is therefore computationally intractable. We propose instead a simple suboptimal method that greedily optimizes the SIR, coefficient-by-coefficient. Simulations show that this greedy approach provides substantial SIR gains over the naive approach, with SIR growing polynomially in the number of antennas. We derive analytical bounds that indicate that even larger SIR gains (exponential in the number of antennas) are potentially achievable, so that finding tractable algorithms that improve upon our suboptimal approach is an important open problem.