gebhart/patrepeval huggingface dataset:
Role of the Jun Kinase Pathway in the Regulation of c-Jun Expression and Apoptosis in Sympathetic Neurons (1998)

When deprived of nerve growth factor (NGF), developing sympathetic neurons die by apoptosis. This death is associated with an increase in the level of c-Jun protein and is blocked by expression of a c-Jun dominant negative mutant. Here we have investigated whether NGF withdrawal activates Jun kinases, a family of stress-activated protein kinases that can stimulate the transcriptional activity of c-Jun by phosphorylating serines 63 and 73 in the transactivation domain and which can activate c-jun gene expression. We found that sympathetic neurons contained high basal levels of Jun kinase activity that increased further after NGF deprivation. In contrast, p38 kinase, another stress-activated protein kinase that can also stimulate c-jun gene expression, was not activated after NGF withdrawal. Consistent with Jun kinase activation, we found using a phospho-c-Jun-specific antibody that c-Jun was phosphorylated on serine 63 after NGF withdrawal. Furthermore, expression of a constitutively active form of MEK kinase 1 (MEKK1), which strongly activates the Jun kinase pathway, increased c-Jun protein levels and c-Jun phosphorylation and induced apoptosis in the presence of NGF. This death could be prevented by co-expression of SEKAL, a dominant negative mutant of SAPK/ERK kinase 1 (SEK1), an activator of Jun kinase that is a target of MEKK1. In contrast, expression of SEKAL alone did not prevent c-Jun expression, increases in c-Jun phosphorylation, or cell death after NGF withdrawal. Thus, activation of Jun kinase and increases in c-Jun phosphorylation and c-Jun protein levels occur at the same time after NGF withdrawal, but c-Jun levels and phosphorylation are regulated by an SEK1-independent pathway.
Dependence of the SET switching variability on the initial state in HfOx‐based ReRAM (2015)

For any application of redox‐based resistive switching devices understanding of variability is of major interest. In this work, we analyze the dependence of the SET switching time in pulse measurements of TiN/HfO x /Pt devices on the initial state before switching. The distribution of the measured SET times covers up to seven decades in one cell. A stochastic as well as a deterministic variability component are identified by relating the initial HRS resistance – obtained from a READ pulse and from the SET pulse for comparison – to the SET time. The different resulting correlations to the SET time for the two descriptions of the initial resistance are analyzed and linked to the polarity and voltage dependence of the HRS. In addition, the origin of the resistance variation is discussed.
CHEMICAL AND BIOLOGICAL DESCRIPTOR INTEGRATION IMPROVES COMPUTATIONAL MODELING OF IN VIVO RAT TOXICITY. (2015)

Computational toxicology is a new discipline in the area of computational molecular sciences, which is rapidly developing as a result of the public interest stirred by several European and US initiatives. Here, we report the use of primary high throughput screening (HTS) data as biological descriptors to complement the chemical descriptors for the modelling of the acute toxicity. The combination of biological and chemical descriptors was performed on the median lethal dose following oral administration in rats (rat LD50). The hybrid model developed based on chemical and biological descriptors is superior to models based on the chemical or biological description alone. Using this model, besides the accurately prediction of a compound's toxicity we also identified molecular fragments whose presence may contribute to increase or decrease of the toxicity.
Combined Oral Contraceptives and Sexual Function in Women—a Double-Blind, Randomized, Placebo-Controlled Trial (2016)

This study shows no negative impact of a levonorgestrel-containing oral contraceptive on overall sexual function, although three of seven sexual function domains were adversely affected.
Silicon-rich silicon nitride CMOS platform for integrated optical phased arrays (2021)

Silicon nitride (SiNx), an associated CMOS photonics enabling material, provides a promising and complementary photonic platform for the development of low-cost CMOS compatible waveguides and related photonic components. We propose a 16 element - 2D scanning optical phased array circuit based on a Si-rich core, which reconciliates the requirements of power handling and field-of-view for automotive LiDAR. This dispersive optical phased array consists of wavelength-dependent grating coupler antenna arrays and spiral-delay lines that allow achieving a field-of-view of (35°x 17°) and an angular resolution of (0.15°x1.2°).
GABA and insulin but not nicotinamide augment α- to β-cell transdifferentiation in insulin-deficient diabetic mice (2022)

Our data suggest a role for endogenous insulin and GABA signalling in α-cell plasticity, which is likely to bypass the common nicotinamide-sensitive stem cell differentiation pathway.
A PORTABLE HEMIANOPSIA TESTER (1976)

A pocket-size static perimeter provided with four test lights, one for each quadrant of the visual field, has been constructed and applied to 190 visual fields in 97 patients. The main advantage of the instrument is its ability to disclose hemianopic defects in bedridden and certain sick patients unable to co-operate with other methods, including the confromtation test. This was performed in 12 fields in 7 patients.
QoE-Driven Cross-Layer Optimization for High Speed Downlink Packet Access (2009)

This paper proposes a Quality of Experience (QoE) based cross-layer design (CLD) framework for High Speed Downlink Packet Access (HSDPA). The proposed scheme aims at maximizing the user satisfaction by taking advantage of the link adaptation mechanism of HSDPA and the rate adaptation capability of multimedia applications. The main contributions of the paper are as follows. First, we describe the multiuser rate region of HSDPA by constructing a long-term radio link layer model. Next, we formulate multimedia QoE by constructing long-term utility functions, describe the multiuser utility space and derive its properties. We show analytically that the maximization of the sum of utility (max-MOS) can be efficiently solved by a fast greedy algorithm which searches only through the boundary of the utility space. We investigate two alternatives to the max-MOS approach, which introduce additional fairness in the system. We compare our proposed QoE-based cross layer optimization schemes to a system that is configured to maximize the overall throughput. For the sake of completeness, we also compare our approaches to a non-optimized HSDPA system. The performance comparison is made by simulation using a software implementation of an actually deployed HSDPA system. Results show that our QoE-based approach leads to significantly improved user perceived quality compared to the other approaches.
Selection of Gene-Marked Tumor Infiltrating Lymphocytes from Post-Treatment Biopsies: A Case Study (1990)

Patients with malignant melanoma have been treated with interleukin-2 (IL-2) and tumor-infiltrating lymphocytes (TIL) marked by retroviral gene transduction. The retroviral vector contained a gene coding for the bacterial enzyme neomycin phosphotransferase, such that transduced TIL expressing the enzyme could survive otherwise toxic concentrations of the neomycin analogue G418. For 1 patient, who exhibited a complete regression of cancer after treatment with TIL, lymphocytes from post-treatment blood and tumor biopsies were cultured in IL-2, and transduced TIL were recovered by G418 selection. Analysis of T-cell receptor heterogeneity indicated that the transduced TIL recovered from the tumor biopsy were different from TIL that were kept strictly in vitro and selected in G418. The selection process required weeks in culture, during which time control cultures changed radically in subset composition, so there was also a simultaneous selection for long-term in vitro growth advantage. It cannot be certain that the TIL subsets preferentially recovered from the tumor biopsy corresponded to those that mediated complete elimination of tumor in this patient.
A Framework to Evaluate Ethical Considerations with ML-HCA Applications—Valuable, Even Necessary, but Never Comprehensive (2020)

This article refers to:Identifying Ethical Considerations for Machine Learning Healthcare Applications
Synthesis, Structure−Activity Relationships, and in Vivo Evaluations of Substituted Di-tert-butylphenols as a Novel Class of Potent, Selective, and Orally Active Cyclooxygenase-2 Inhibitors. 2. 1,3,4- and 1,2,4-Thiadiazole Series (1999)

Two isoforms of the cyclooxygenase (COX) enzyme have been identified: COX-1, which is expressed constitutively, and COX-2, which is induced in inflammation. Recently, it has been shown that selective COX-2 inhibitors have antiinflammatory activity and lack the GI side effects typically associated with NSAIDs. Initial mass screening and subsequent SAR studies have identified 6b (PD164387) as a potent, selective, and orally active COX-2 inhibitor. It had IC50 values of 0.14 and 100 μM against recombinant human COX-2 and purified ovine COX-1, respectively. It inhibited COX-2 activity in the J774A.1 cell line with an IC50 of 0.18 μM and inhibited COX-1 activity in platelets with an IC50 of 3.1 μM. The choline salt of compound 6b was also orally active in vivo with an ED40 of 7.1 mg/kg in the carrageenan footpad edema (CFE) assay. In vivo studies in rats at a dose of 100 mg/kg showed that this compound inhibited gastric prostaglandin E2 (PGE2) production in gastric mucosa by 77% but caused minimal GI damage. SAR studies of this chemical series revealed that the potency and selectivity are very sensitive to minor structural changes.
On the breakup of a thin liquid film subject to interfacial shear (2004)

The breakup of a thin non-evaporating liquid film that is either flowing down or climbing on a vertical or inclined surface and subject to cocurrent or countercurrent interfacial shear (or gas flow) is investigated analytically. Analytical expressions for the dimensionless liquid film thickness, $\Delta_{\hbox{\scriptsize\it min}}$ , and wetting rate, $\Gamma_{\hbox{\scriptsize\it min}}$ , at breakup are derived based on the minimization of the total energy of a stable rivulet, formed following the film breakup. For a downflowing liquid film, increasing the cocurrent interfacial shear (or gas velocity) or decreasing the equilibrium contact angle, $\theta_{o}$ , decreases both $\Delta_{\hbox{\scriptsize\it min}}$ and $\Gamma _{\hbox{\scriptsize\it min}}$ , below their values with zero interfacial shear. Conversely, increasing the countercurrent interfacial shear or $\theta_{o}$ , increases both $\Delta_{\hbox{\scriptsize\it min}}$ and $\Gamma_{\hbox{\scriptsize\it min}}$ , above their values with zero interfacial shear. The predictions of $\Delta _{\hbox{\scriptsize\it min}}$ and $\Gamma _{\hbox{\scriptsize\it min}}$ for a climbing water film on a vertical surface are in good agreement with reported experimental data for a wide range of cocurrent gas velocities.
6.3-Tb/s Unrepeatered Transmission over 402-km Fiber using High Power Yb-free Clad-pumped L-band EDFA (2014)

Unrepeatered transmission of 6.3-Tb/s (63x128-Gb/s) signals over 402-km of effective-area (Aeff) managed fiber link is achieved by employing high power Yb-free clad-pumped L-band EDFA and remote optically pumped amplifier, which is counter-propagating 2nd-order Raman pumped.
Diastereodifferentiating Photocyclodimerization of 2-Anthracenecarboxylates Tethered to a Cyclic Tetrasaccharide Scaffold: Critical Control of Photoreactivity and Stereoselectivity (2013)

From a complex mixture of mono- and di-2-anthracenecarboxylic acid (AC) esters of cyclic nigerosylnigerose (CNN), two monoesters (2(B) and 6(A)) and four diesters in which AC was introduced on the transannular B/D (2(B)2(D)), adjacent A/B and A/D (6(A)2(B) and 6(A)2(D)), and same B/B (2(B)3(B)) nigerose rings were isolated. Possessing two ACs at distant positions, 2(B)2(D) and 6(A)2(D) showed negative Cotton effects for the (1)Bb band, the intensities of which were stronger than that of 6(A). 2(B)2(D) and 6(A)2(D) slowly photocyclodimerized to give HH dimers 3* and 4 with 57% and 81% HH selectivity, respectively, which were appreciably higher than that for 6(A) (34%), while the enantiomeric excesses (ee's) of anti-HH dimer 3* were 2% and -18%, respectively. In contrast, 6(A)2(B) and 2(B)3(B) carrying two ACs on adjacent A and B rings or at vicinal positions on the B ring, respectively, exhibited strong positive CD couplets, the amplitudes of which amounted to 97 and 409 M(-1) cm(-1), respectively. Upon irradiation, 6(A)2(B) afforded 3* with -62% ee and 4 in 96% combined yield, whereas 2(B)3(B) gave almost exclusively 3* with -99% ee in 96% yield, likely as a result of the introduction of two ACs at the vicinal positions of the rigid CNN scaffold.
Gold-in-copper at low *CO coverage enables efficient electromethanation of CO2 (2021)

The renewable-electricity-powered CO<sub>2</sub> electroreduction reaction provides a promising means to store intermittent renewable energy in the form of valuable chemicals and dispatchable fuels. Renewable methane produced using CO<sub>2</sub> electroreduction attracts interest due to the established global distribution network; however, present-day efficiencies and activities remain below those required for practical application. Here we exploit the fact that the suppression of *CO dimerization and hydrogen evolution promotes methane selectivity: we reason that the introduction of Au in Cu favors *CO protonation vs. C-C coupling under low *CO coverage and weakens the *H adsorption energy of the surface, leading to a reduction in hydrogen evolution. We construct experimentally a suite of Au-Cu catalysts and control *CO availability by regulating CO<sub>2</sub> concentration and reaction rate. This strategy leads to a 1.6× improvement in the methane:H<sub>2</sub> selectivity ratio compared to the best prior reports operating above 100 mA cm<sup>-2</sup>. We as a result achieve a CO<sub>2</sub>-to-methane Faradaic efficiency (FE) of (56 ± 2)% at a production rate of (112 ± 4) mA cm<sup>-2</sup>.
TiFL: A Tier-based Federated Learning System (2020)

Federated Learning (FL) enables learning a shared model acrossmany clients without violating the privacy requirements. One of the key attributes in FL is the heterogeneity that exists in both resource and data due to the differences in computation and communication capacity, as well as the quantity and content of data among different clients. We conduct a case study to show that heterogeneity in resource and data has a significant impact on training time and model accuracy in conventional FL systems. To this end, we propose TiFL, a Tier-based Federated Learning System, which divides clients into tiers based on their training performance and selects clients from the same tier in each training round to mitigate the straggler problem caused by heterogeneity in resource anddata quantity. To further tame the heterogeneity caused by non-IID (Independent and Identical Distribution) data and resources, TiFL employs an adaptive tier selection approach to update the tiering on-the-fly based on the observed training performance and accuracy. We prototype TiFL in a FL testbed following Google's FL architecture and evaluate it using the state-of-the-art FL benchmarks. Experimental evaluation shows that TiFL outperforms the conventional FL in various heterogeneous conditions. With the proposed adaptive tier selection policy, we demonstrate that TiFL achieves much faster training performance while achieving the same or better test accuracy across the board.
BRD4: A BET(ter) target for the treatment of AML? (2014)

Click to increase image sizeClick to decrease image sizeKeywords:: targeted therapyAMLleukemic stem cellsBRD4JQ1This article is related to:
Industrial Robot Trajectory Tracking Control Using Multi-Layer Neural Networks Trained by Iterative Learning Control (2021)

Fast and precise robot motion is needed in many industrial applications. Most industrial robot motion controllers allow externally commanded motion profiles, but the trajectory tracking performance is affected by the robot dynamics and joint servo controllers, to which users have no direct access and about which they have little information. The performance is further compromised by time delays in transmitting the external command as a setpoint to the inner control loop. This paper presents an approach for combining neural networks and iterative learning controls to improve the trajectory tracking performance for a multi-axis articulated industrial robot. For a given desired trajectory, the external command is iteratively refined using a high-fidelity dynamical simulator to compensate for the robot inner-loop dynamics. These desired trajectories and the corresponding refined input trajectories are then used to train multi-layer neural networks to emulate the dynamical inverse of the nonlinear inner-loop dynamics. We show that with a sufficiently rich training set, the trained neural networks generalize well to trajectories beyond the training set as tested in the simulator. In applying the trained neural networks to a physical robot, the tracking performance still improves but not as much as in the simulator. We show that transfer learning effectively bridges the gap between simulation and the physical robot. Finally, we test the trained neural networks on other robot models in simulation and demonstrate the possibility of a general purpose network. Development and evaluation of this methodology are based on the ABB IRB6640-180 industrial robot and ABB RobotStudio software packages.
Predictive radiogenomics modeling of EGFR mutation status in lung cancer (2017)

Molecular analysis of the mutation status for EGFR and KRAS are now routine in the management of non-small cell lung cancer. Radiogenomics, the linking of medical images with the genomic properties of human tumors, provides exciting opportunities for non-invasive diagnostics and prognostics. We investigated whether EGFR and KRAS mutation status can be predicted using imaging data. To accomplish this, we studied 186 cases of NSCLC with preoperative thin-slice CT scans. A thoracic radiologist annotated 89 semantic image features of each patient's tumor. Next, we built a decision tree to predict the presence of EGFR and KRAS mutations. We found a statistically significant model for predicting EGFR but not for KRAS mutations. The test set area under the ROC curve for predicting EGFR mutation status was 0.89. The final decision tree used four variables: emphysema, airway abnormality, the percentage of ground glass component and the type of tumor margin. The presence of either of the first two features predicts a wild type status for EGFR while the presence of any ground glass component indicates EGFR mutations. These results show the potential of quantitative imaging to predict molecular properties in a non-invasive manner, as CT imaging is more readily available than biopsies.
Regulation of 4F2 Heavy-Chain Gene Expression During Normal Human T-Cell Activation Can Be Mediated by Multiple Distinct Molecular Mechanisms (1988)

The 4F2 molecule belongs to the set of cell surface antigens which is induced following lectin- or antigen-mediated T-cell activation. The increase in 4F2 cell surface expression following lectin-mediated stimulation has been shown to be accompanied by a parallel increase in the steady-state levels of 4F2 heavy-chain (4F2HC) mRNA. The studies described in this report were designed to further elucidate the molecular mechanisms responsible for induction of 4F2HC gene expression following activation of normal resting human peripheral blood T cells. The low levels of mature 4F2HC mRNA in resting T cells were shown to be the result of a block to transcription elongation within the exon 1-intron 1 region of the 4F2HC gene rather than promoter inactivity. Phorbol myristate acetate stimulation of resting T cells resulted in a 20-fold increase in steady-state 4F2HC mRNA levels which was mediated by removal of this block to transcription elongation. The phorbol myristate acetate-induced increase in 4F2HC gene expression is distinct from previously described AP-1-mediated, phorbol ester-induced gene expression in that it requires new protein synthesis. Treatment of resting T cells with ionomycin plus PMA resulted in a 60-fold increase in 4F2HC mRNA levels. This induction was mediated by both an increase in promoter utilization and removal of the block to transcription elongation. Finally, by increasing the half-life of 4F2HC mRNA, cycloheximide treatment of resting T cells induced an approximately five fold increase in the levels of 4F2HC gene expression, although the physiologic significance of this mechanism remains unclear. These results demonstrate that the level of 4F2HC gene expression in normal peripheral blood T cells can be regulated by at least three distinct molecular pathways: (i) changes in promoter utilization, (ii) modulation of a block to transcription elongation, and (iii) alteration in mRNA stability.
Valorization of polybutadiene waste streams to unsaturated macrocycles with Ru metathesis catalysis (2015)

status: Accepted
Investigation of a hybrid localization technique using Received Signal Strength and Direction of arrival (2013)

This paper investigates a hybrid technique that uses a combined version of Received Signal Strength (RSS) and Direction of arrival (DOA) localization techniques. Simulation results prove that using the hybrid technique in one node increases the localization accuracy and provides the node with the capability of localizing other nodes by itself without any assistance from other nodes. The performance of the hybrid technique has been evaluated under both Additive White Gaussian Noise (AWGN) and Rayleigh channel conditions. Moreover, the study shows when to use the hybrid node, and where to place such node in a given environment to get the optimum results.
Light that spins inside fibers: Applications from microscopy to telecommunications (2013)

We present a class of fibers that enable the generation and propagation of optical vortices. We review recent results obtained with such fibers in fields as different super-resolution microscopy and telecom information-capacity scaling.
Phenotypic Heterogeneity of Hemostasis in Severe Hemophilia (2015)

A reduction in bleeding pattern and arthropathy appears to be observed in approximately 10% of the patients with severe hemophilia (< 1% clotting factor activity). These patients rarely bleed and do not always need prophylactic therapy of therapeutic products, resulting in the wide range of joint damage seen in patients with severe hemophilia. The cause(s) of this phenotypic heterogeneity has been investigated in many studies till date, but remains to be completely solved. The large heterogeneity of the clinical phenotype in severe hemophilia seems to be multifactorial, including variation in the levels of various procoagulant and anticoagulant factors, the balance between the coagulation and fibrinolysis systems, pharmacokinetics of therapeutic products, environmental factors including lifestyle activity, and the limitation of measurement at lower levels of clotting factors. As an approach toward clarification, studies should be designed to evaluate a homogenous cohort of hemophilic A patients with an intron 22 inversion who produce no factor VIII. In the future, by a combination of the measurement of lower levels of clotting factors and the evaluation of global clotting function, it might be possible to better grasp the potential of hemostatic coagulation in individual hemophilia patients, which should in turn be useful for the prediction of bleeding phenotype and the designation of adequate and long-term hemostatic management throughout their life.