gebhart/patrepeval huggingface dataset:
Murine Lyme Arthritis Development Mediated by p38 Mitogen-Activated Protein Kinase Activity (2002)

Borrelia burgdorferi, the Lyme disease agent, causes joint inflammation in an experimental murine model. Inflammation occurs, in part, due to the ability of B. burgdorferi to induce the production of proinflammatory cytokines and a strong CD4(+) T helper type 1 response. The mechanisms by which spirochetes induce these responses are not completely known, although transcription factors, such as NF-kappa B in phagocytic cells, initiate the proinflammatory cytokine burst. We show here that the mitogen-activated protein (MAP) kinase of 38 kDa (p38 MAP kinase) is involved in the proinflammatory cytokine production elicited by B. burgdorferi Ags in phagocytic cells and the development of murine Lyme arthritis. B. burgdorferi Ags activated p38 MAP kinase in vitro, and the use of a specific inhibitor repressed the spirochete-induced production of TNF-alpha. The infection of mice that are deficient for a specific upstream activator of the kinase, MAP kinase kinase 3, resulted in diminished proinflammatory cytokine production and the development of arthritis, without compromising the ability of CD4(+) T cells to respond to borrelial Ags or the production of specific Abs. Overall, these data indicated that the p38 MAP kinase pathway plays an important role in B. burgdorferi-elicited inflammation and point to potential new therapeutic approaches to the treatment of inflammation induced by the spirochete.
Learning to Generate Fair Clusters from Demonstrations (2021)

Fair clustering is the process of grouping similar entities together, while satisfying a mathematically well-defined fairness metric as a constraint. Due to the practical challenges in precise model specification, the prescribed fairness constraints are often incomplete and act as proxies to the intended fairness requirement. Clustering with proxies may lead to biased outcomes when the system is deployed. We examine how to identify the intended fairness constraint for a problem based on limited demonstrations from an expert. Each demonstration is a clustering over a subset of the data. We present an algorithm to identify the fairness metric from demonstrations and generate clusters using existing off-the-shelf clustering techniques, and analyze its theoretical properties. To extend our approach to novel fairness metrics for which clustering algorithms do not currently exist, we present a greedy method for clustering. Additionally, we investigate how to generate interpretable solutions using our approach. Empirical evaluation on three real-world datasets demonstrates the effectiveness of our approach in quickly identifying the underlying fairness and interpretability constraints, which are then used to generate fair and interpretable clusters.
Comparison of a Sleep Quality Index between Normal and Obstructive Sleep Apnea Patients (2005)

This paper aimed at developing an index, called Sleep Index, to assess the quality of sleep in normal and obstructive sleep apnea (OSA) subjects. The Sleep Index was designed to be directly proportional to the summation of product of the number seconds spent in each stage of sleep and the selected weighting coefficient of each sleep stage. It was also inversely proportional to the product of total number of sleep stage shifts and the total number of seconds spent in all stages of sleep. In order to test the proposed index, data from eleven previously diagnosed sleep apnea subjects (6 females and 5 males; Age: 50 ± 8.94; Body Mass Index (BMI): 31.70 ± 6.97) and 14 normal subjects (8 females and 6 males; Age: 46.43 ± 9.61; BMI: 25.54<sup>1</sup>± 3.06<sup>1</sup>) were used. All the subjects underwent nocturnal polysomnography (NPSG) at an accredited sleep center. Statistical testing of the Sleep Index showed that its mean was significantly different for normal and OSA subjects (p<0.04). The Sleep Index values were higher for normal subjects than for sleep apnea subjects. This was in part due to the higher number of sleep stage shifts in OSA subjects compared to normal subjects. Therefore, higher Sleep Index values reflect better sleep quality. The number of sleep stage shifts should be higher for sleep apnea subjects as they frequently experience sleep arousal and sleep continuity is impaired, resulting in daytime sleepiness.
New efficient and long life catalyst for glycerol dehydration to acrolein (2012)

International @ RAFFINAGE+SLO:JMI
Multichannel HR-NMF for modelling convolutive mixtures of non-stationary signals in the time-frequency domain (2013)

Several probabilistic models involving latent components have been proposed for modelling time-frequency (TF) representations of audio signals (such as spectrograms), notably in the nonnegative matrix factorization (NMF) literature. Among them, the recent high resolution NMF (HR-NMF) model is able to take both phases and local correlations in each frequency band into account, and its potential has been illustrated in applications such as source separation and audio inpainting. In this paper, HR-NMF is extended to multichannel signals and to convolutive mixtures. A fast variational expectation-maximization (EM) algorithm is proposed to estimate the enhanced model. This algorithm is applied to a stereophonic piano signal, and proves capable of accurately modelling reverberation and restoring missing observations.
RePAD: Real-time Proactive Anomaly Detection for Time Series (2020)

During the past decade, many anomaly detection approaches have been introduced in different fields such as network monitoring, fraud detection, and intrusion detection. However, they require understanding of data pattern and often need a long off-line period to build a model or network for the target data. Providing real-time and proactive anomaly detection for streaming time series without human intervention and domain knowledge is highly valuable since it greatly reduces human effort and enables appropriate countermeasures to be undertaken before a disastrous damage, failure, or other harmful event occurs. However, this issue has not been well studied yet. To address it, this paper proposes RePAD, which is a Real-time Proactive Anomaly Detection algorithm for streaming time series based on Long Short-Term Memory (LSTM). RePAD utilizes short-term historic data points to predict and determine whether or not the upcoming data point is a sign that an anomaly is likely to happen in the near future. By dynamically adjusting the detection threshold over time, RePAD is able to tolerate minor pattern change in time series and detect anomalies either proactively or on time. Experiments based on two time series datasets collected from the Numenta Anomaly Benchmark demonstrate that RePAD is able to proactively detect anomalies and provide early warnings in real time without human intervention and domain knowledge.
Relation between magnetoresistance and nanostructure of current-perpendicular-to-plane giant-magnetoresistance film with current-confined-path nano-oxide layer (2008)

Nanostructure of a current-perpendicular-to-plane giant-magnetoresistance film with a current-confined-path (CCP) nano-oxide layer was analyzed by high-resolution transmission electron microscopy and three-dimensional atom probe. It was found that the CCP of a film with a higher magnetoresistance (MR) ratio has better crystalline orientation and higher purity than the CCP of a film with a smaller MR ratio. Moreover, the free layer on the CCP of a film with a high MR ratio is well crystallized. Both the CCP with the good crystalline orientation and high purity and the well-crystallized free layer diminish the diffusive electron scattering, which improves an MR ratio.
Noise variance analysis using a flat panel x‐ray detector: A method for additive noise assessment with application to breast CT applications (2010)

The existence of the signal-independent additive noise is the primary cause for a quadratic relationship between bCT noise variance and the inverse of radiation dose at the detector. With the knowledge of the additive noise contribution to experimentally acquired images, system modifications can be made to reduce the impact of additive noise and improve the quantum noise efficiency of the bCT system.
Inside Cover: Lewis Acid Activated Synthesis of Highly Substituted Cyclopentanes by the N‐Heterocyclic Carbene Catalyzed Addition of Homoenolate Equivalents to Unsaturated Ketoesters (Angew. Chem. Int. Ed. 7/2011) (2011)

A highly diastereo- and enantioselective N-heterocyclic carbene catalyzed/titanium(IV)-mediated homoenolate addition to β,γ-unsaturated α-ketoesters to assemble cyclopentanols with four contiguous stereogenic centers is described by Scheidt and co-workers in their Communication on page 1678 ff. The Lewis acid is essential for the reaction and a wide range of β,γ-unsaturated α-ketoesters and enals are tolerated, with the products obtained in 52–85% yield and up to 99% ee.
Variational Bayesian inversion of seismic attributes jointly for geologic facies and petrophysical rock properties (2020)

ABSTRACT Seismic attributes (derived quantities) such as P-wave and S-wave impedances and P-wave to S-wave velocity ratios may be used to classify subsurface volume of rock into geologic facies (distinct lithology-fluid classes) using pattern recognition methods. Seismic attributes may also be used to estimate subsurface petrophysical rock properties such as porosity, mineral composition, and pore-fluid saturations. Both of these estimation processes are conventionally carried out independent of each other and involve considerable uncertainties, which may be reduced significantly by a joint estimation process. We have developed an efficient probabilistic inversion method for joint estimation of geologic facies and petrophysical rock properties. Seismic attributes and petrophysical properties are jointly modeled using a Gaussian mixture distribution whose parameters are initialized by unsupervised learning using well-log data. Rock-physics models may be used in our method to augment the training data if the existing well data are limited; however, this is not required if sufficient well data are available. The inverse problem is solved using the Bayesian paradigm that models uncertainties in the form of probability distributions. Probabilistic inference is performed using variational optimization, which is a computationally efficient deterministic alternative to the commonly used sampling-based stochastic inference methods. With the help of a real data application from the North Sea, we find that our method is computationally efficient, honors expected spatial correlations of geologic facies, allows reliable detection of convergence, and provides full probabilistic results without stochastic sampling of the posterior distribution.
Bcl-2 expression inhibits prostaglandin E2-mediated apoptosis in B cell lymphomas (1996)

Apoptosis is a critical mechanism in the maturation and maintenance of the immune system. However, the process by which cells die remains poorly understood. The proto-oncogene bcl-2 is considered important in determining whether cells enter an apoptotic pathway or survive. In this report, we first examined the differential sensitivity of immature (CH31) and mature (CH12) B cell lymphomas to growth inhibition by PGE2. The CH31 cell line was growth inhibited and underwent apoptosis in response to PGE2, unlike its mature counterpart, CH12. Furthermore, endogenous levels of the anti-apoptotic protein Bcl-2 in CH31 cells were low compared with CH12. To further investigate the role of Bcl-2 in PGE2- and cAMP-mediated cell death, a retroviral vector bearing the human bcl-2 gene was introduced into CH31. High expression of Bcl-2 in CH31 had no effect on growth inhibition induced by PGE2 or dibutyryl cAMP. In contrast, increased expression of Bcl-2 completely inhibited PGE2- and cAMP-mediated DNA fragmentation and nuclear condensation. Finally, cell cycle analysis of Bcl-2-expressing CH31 cells demonstrated that PGE2 increased the percentage of cells in G1, and analysis of synchronized populations revealed that PGE2 acts at all phases of the cell cycle to delay normal progression. These results support the hypothesis that apoptosis induced through PGE2 and cAMP signaling is sensitive to regulation by Bcl-2 in CH31 B cell lymphomas. Furthermore, unlike apoptosis, regulation of PGE2- and cAMP-mediated growth inhibition in B lineage cells is a distinct and Bcl-2-independent mechanism.
Novel Foot Progression Angle Algorithm Estimation via Foot-Worn, Magneto-Inertial Sensing (2016)

This study enables future wearable systems gait research to assess or train walking patterns outside a laboratory setting in natural walking environments.
Role of bulge cells in wound healing: possible implications for hidradenitis suppurativa (2006)

The hair follicle bulge harbors a cluster of quiescent epithelial stem cells, which generate the new lower hair follicle during follicle cycling. The role of bulge cells for maintenance of the hair follicle and epidermis during normal homeostasis and after wounding remains controversial. To address these questions, we targeted the suicide gene, thymidine kinase (TK), or CrePR recombinase to hair follicle bulge cells using a K15 promoter. Administration of ganciclovir to K15‐TK mice caused their death due to gastrointestinal injury. We then treated immunodeficient mice carrying K15‐TK skin grafts with ganciclovir. This resulted in injury of bulge cells within several days. Loss of hair and permanent injury to hair follicles ensued. Dermal scarring was also present. The epidermis without follicles survived for several months. To further assess the contribution of bulge cells to epidermis, we used double transgenic K15‐crePR1, R26R mice. After 5 days of treatment with RU‐486 (time 0), bulge cells and a small fraction of epidermal cells expressed LacZ under control of the ROSA promoter. To determine whether bulge cells moved into the epidermis under normal homeostatic conditions, we counted labeled epidermal basal cells at times 0, 30 days, and 180 days. We found that the percentage of labeled epidermal basal cells (approximately 1%) remained constant, indicating an absence of cell movement from the bulge to the epidermis. After punch wounding, bulge progeny were detected in a radial pattern in the re‐epithelialized area. Radial streaks of bulge cell progeny emanated from the hair follicles at the wound edge. Bulge cell progeny proliferated and expressed normal epidermal differentiation markers such as keratin 10 and loricrin. Overall, these results indicate that follicular stem cells in the bulge are necessary for hair follicle survival and that these cells functionally contribute to epidermal regeneration in response to wounding; however, the epidermis self‐renews autonomously of the bulge under normal conditions. The role of bulge cells in hidradenitis suppurativa (HS) is not known; however, pathological studies suggest aberrant proliferation of the hair follicle may accompany HS and inappropriate stem cell activation and differentiation could be a component of this disorder. The K15‐crePR1 transgenic mouse will serve as a powerful tool for evaluating the role of hair follicle stem cells in mouse models of HS. Studying hair follicle stem cells with recently defined markers for these cells will be useful for evaluating stem cell behavior in HS lesions.
Structure, ferroelectric properties, and magnetic properties of the La-doped bismuth ferrite (2008)

Bi 1 − x La x Fe O 3 ceramics with x=0, 0.1, 0.2, and 0.3 have been synthesized by solid state reaction, starting from metal oxides. A series of structure transformations is found to depend upon the doping level. Below 10% La doping, Bi1−xLaxFeO3 maintains the rhombohedral structure of BiFeO3. However, for Bi0.8La0.2FeO3 and Bi0.7La0.3FeO3, the structures change to the orthorhombic and tetragonal, respectively. La doping significantly reduces electric leakage and leads to successful observation of electrical polarization hysteresis loops. Doping with La also enhances the ferromagnetic moment, due to the broken cycloid spin structure caused by the changes in the crystalline structure.
Cochlear implantation after transmastoid labyrinthectomy (1989)

Hearing rehabilitation with an intracochlear prosthesis is well documented in patients who have an intact otic capsule prior to implantation. However, the suitability for implantation of patients who have undergone extensive procedures involving the otic capsule such as labyrinthectomy has not been directly addressed. This report documents a case of a patient deafened by a transmastoid labyrinthectomy who subsequently received a cochlear implant. Postimplantation performance of this patient was compared with the performance of three other postlingual implant recipients. The results suggest that labyrinthectomy is not a contraindication to auditory rehabilitation by a cochlear implant. The implications of implantation in a surgically manipulated otic capsule are discussed.
Simultaneous on-line vacuum single- and multi-photon ionization on an orthogonal acceleration time-of-flight mass spectrometer platform (2022)

The development of orthogonal acceleration time-of-flight (oa-tof) technology is driven forward due to higher mass accuracy and resolving power than conventional linear/reflectron tof instruments. This is achieved with a more accurate definition of starting energies and coordinates of ions by spatial separation of ion generation and orthogonal ion extraction. Consequently, the ability to cover the whole mass spectral range without scanning is not given anymore. Therefore, continuous ion sources are favored for ensuring high duty cycles and thus high temporal resolution. For pulsed ion sources, high repetition rates are mandatory for covering large <i>m</i>/<i>z</i> ranges without losing their high temporal resolution. We have combined an oa-tof with deuterium lamp single-photon ionization (SPI) as a continuous ion source together with a pulsed 2000 Hz excimer (KrF) laser for resonance enhanced multi-photon ionization (REMPI). These two ionization techniques can be used simultaneously. To the best of our knowledge, this system is the first of its kind in combining a vacuum pulsed ionization source with an oa-tof instrument without any other ion storage hardware. The combination of a soft broadband ionization for organics (SPI) in combination with a very sensitive and selective soft ionization (REMPI) can be used for covering the whole mass range or in targeted on-line monitoring cases one or several smaller mass ranges. To demonstrate the simultaneous SPI/REMPI-oa-tof technique, two applicative areas are explored: on-line monitoring of coffee roast gas emissions and e-cigarette vapor. The complementary information from SPI and REMPI signals are combined in a way to exploit the advantages of both ionization types. In a further development step, a second data acquisition card is built into the system. This modification allows the independent storage of data from both ionization methods without mixing. For demonstration, a third example with a GC measurement is provided. The last example shows the possibility of modified sensitivities for different mass regions in REMPI data acquisition without affecting the SPI channel. The newly developed system shows high robustness in terms of measurements in real industrial environments. The simultaneous measurement technique provides a higher density of information in a single measurement, saving time and resources.
Continuous flow homogeneous hydroformylation of alkenes using supercritical fluids (2005)

The hydroformylation of long chain alkenes, carried out as a continuous flow process by using a catalyst made in situ from [Rh(CO)2(2,4-pentanedioate)] and [1-propyl-3-methylimidazolium][Ph2P(3-C6H4SO3)] dissolved in 1-octyl-3-methylimidazolium bis(trifluoromethylsulfonamide), is reviewed. The substrates are introduced into and the products are removed from the reactor dissolved in continuously flowing supercritical carbon dioxide. Optimisation studies allow long term operation with rates up to 500 catalyst turnovers h−1 and rhodium leaching into the product as low as 0.012 ppm. Using a different ligand based on the xantphos skeleton, linear ∶ branched ratios in the product aldehydes can be as high as 40 ∶ 1, but the rate is somewhat lower (272 h−1) and the rhodium retention is slightly less efficient. By removing the ionic liquid and dissolving the catalyst in the mixture of products and substrates that develops during the reaction, it is possible to carry out the reaction at much lower pressures (125 bar). 1-alkyl-3-methylimidazolium salts of [Ph2P(3-C6H4SO3)] are used as ligands and the success of the reaction depends crucially on the alkyl chain employed in the imidazolium cation. Too long a chain causes large amounts of rhodium leaching, whilst too small a chain causes the solubility of the ligand to be too low so that the reaction is very poor and unliganded rhodium is rapidly extracted from the system. The best results are obtained using a pentyl chain, which gives a rate of 162 h−1 and rhodium leaching of 0.1–0.5 ppm. Comparisons of these systems with current commercial systems are made and consideration is given to the design of a plant suitable for operating these reactions in a totally emissionless fashion.
Sorafenib administered using a high-dose, pulsatile regimen in patients with advanced solid malignancies: a phase I exposure escalation study (2020)

Treatment with high-dose, once weekly sorafenib administration resulted in dose-limiting toxicity precluding dose escalation above the exposure cohort of 125-150 mg/L/h. Drug monitoring was a successful strategy to pursue a target exposure.
Approximating Minimum Subset Feedback Sets in Undirected Graphs with Applications (2000)

Let G=(V,E) be a weighted undirected graph where all weights are at least one. We consider the following generalization of feedback set problems. Let $S \subset V$ be a subset of the vertices. A cycle is called interesting if it intersects the set S. A subset feedback edge (vertex) set is a subset of the edges (vertices) that intersects all interesting cycles. In minimum subset feedback problems the goal is to find such sets of minimum weight. This problem has a variety of applications, among them genetic linkage analysis and circuit testing. The case in which S consists of a single vertex is equivalent to the multiway cut problem, in which the goal is to separate a given set of terminals. Hence, the subset feedback problem is NP-complete and also generalizes the multiway cut problem. We provide a polynomial time algorithm for approximating the subset feedback edge set problem that achieves an approximation factor of two. This implies a $\Delta$-approximation algorithm for the subset feedback vertex set problem, where $\Delta$ is the maximum degree in G. We also consider the multicut problem and show how to achieve an $O(\log \tau^*)$ approximation factor for this problem, where $\tau^*$ is the value of the optimal fractional solution. To achieve the $O(\log \tau^*)$ factor we employ a bootstrapping technique.