gebhart/patrepeval huggingface dataset:
What Is the Best Way to Optimally Parameterize the MPC Cost Function for Vehicle Guidance? (2023)

Model predictive control (MPC) is a promising approach to the lateral and longitudinal control of autonomous vehicles. However, the parameterization of the MPC with respect to high-level requirements such as passenger comfort, as well as lateral and longitudinal tracking, is challenging. Numerous tuning parameters and conflicting requirements need to be considered. In this paper, we formulate the MPC tuning task as a multi-objective optimization problem. Its solution is demanding for two reasons: First, MPC-parameterizations are evaluated in a computationally expensive simulation environment. As a result, the optimization algorithm needs to be as sample-efficient as possible. Second, for some poor parameterizations, the simulation cannot be completed; therefore, useful objective function values are not available (for instance, learning with crash constraints). In this work, we compare the sample efficiency of multi-objective particle swarm optimization (MOPSO), a genetic algorithm (NSGA-II), and multiple versions of Bayesian optimization (BO). We extend BO by introducing an adaptive batch size to limit the computational overhead. In addition, we devise a method to deal with crash constraints. The results show that BO works best for a small budget, NSGA-II is best for medium budgets, and none of the evaluated optimizers are superior to random search for large budgets. Both proposed BO extensions are, therefore, shown to be beneficial.
Ribophorin II regulates breast tumor initiation and metastasis through the functional suppression of GSK3β (2013)

Mutant p53 (mtp53) gain of function (GOF) contributes to various aspects of tumor progression including cancer stem cell (CSC) property acquisition. A key factor of GOF is stabilization and accumulation of mtp53. However, the precise molecular mechanism of the mtp53 oncogenic activity remains unclear. Here, we show that ribophorin II (RPN2) regulates CSC properties through the stabilization of mtp53 (R280K and del126-133) in breast cancer. RPN2 stabilized mtp53 by inactivation of glycogen synthase kinase-3β (GSK3β) which suppresses Snail, a master regulator of epithelial to mesenchymal transition. RPN2 knockdown promoted GSK3β-mediated suppression of heat shock proteins that are essential for mtp53 stabilization. Furthermore, our study reveals that high expression of RPN2 and concomitant accumulation of mtp53 were associated with cancer tissues in a small cohort of metastatic breast cancer patients. These findings elucidate a molecular mechanism for mtp53 stabilization and suggest that RPN2 could be a promising target for anti-CSC therapy.
Data from A Small-Molecule Antagonist of HIF2α Is Efficacious in Preclinical Models of Renal Cell Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;More than 90% of clear cell renal cell carcinomas (ccRCC) exhibit inactivation of the von Hippel–Lindau (pVHL) tumor suppressor, establishing it as the major underlying cause of this malignancy. pVHL inactivation results in stabilization of the hypoxia-inducible transcription factors, HIF1α and HIF2α, leading to expression of a genetic program essential for the initiation and progression of ccRCC. Herein, we describe the potent, selective, and orally active small-molecule inhibitor PT2385 as a specific antagonist of HIF2α that allosterically blocks its dimerization with the HIF1α/2α transcriptional dimerization partner ARNT/HIF1β. PT2385 inhibited the expression of HIF2α-dependent genes, including VEGF-A, PAI-1, and cyclin D1 in ccRCC cell lines and tumor xenografts. Treatment of tumor-bearing mice with PT2385 caused dramatic tumor regressions, validating HIF2α as a pivotal oncogenic driver in ccRCC. Notably, unlike other anticancer agents that inhibit VEGF receptor signaling, PT2385 exhibited no adverse effect on cardiovascular performance. Thus, PT2385 represents a novel class of therapeutics for the treatment of RCC with potent preclincal efficacy as well as improved tolerability relative to current agents that target the VEGF pathway. &lt;i&gt;Cancer Res; 76(18); 5491–500. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Results from International Questionnaires (2007)

A trend to continuous therapies and increased RRT dosage over the last 10 years is shown by the surveys presented, even if scientific evidence is now very necessary as far as definitive RRT indications and prescriptions are concerned.
Electrochemical site-specific functionalization for high resolution multi-target biosensors (2017)

status: Published
Dust and scratch removal in scanned images (2007)

Dust, scratches or hair on originals (prints, slides or negatives) distinctly appear as light or dark artifacts on a scan. These unsightly artifacts have become a major consumer concern. This paper describes an algorithmic solution to the dust and scratch removal task. The solution is divided into two phases: a detection phase and a reconstruction phase. Some scanners have dedicated hardware to detect dust and scratch areas in the original. Without hardware assistance, dust and scratch removal algorithms generally resort to blurring, at the loss of image detail. We present an algorithmic alternative for dust and scratch detection that effectively differentiates between defects and image details. In addition we present reconstruction algorithms, that preserve image sharpness better than available alternatives. For detection we generate a detail-less image in which the defects are "erased". We compare properties of the luminance channel of the input image relative to the detailless image. For reconstruction of the defective areas we suggest both a fast small support algorithm and a large support algorithm, which is better able to mimic the existing image texture.
Qualitätsevaluierung von Physical Unclonable Functions als Schlüsselspeicher (2015)

Silizium-basierte Physical Unclonable Functions (PUFs) sind vergleichsweise neue Security-Primitive, mit denen ein Geheimnis aus Variationen im Fertigungsprozess elektronischer Schaltungen extrahiert werden kann. Hierbei ist jedoch noch nicht abschliesend geklart, wie die Bewertung solcher PUFs aussehen muss, um ein gute Qualitat bezuglich der Unvorhersagbarkeit des Geheimnisses zu gewahrleisten. In dieser Arbeit wird beispielhaft dargestellt, welche Schritte eine Qualitatsevaluierung von PUFs beinhalten konnte. Mithilfe von Entropieschatzung, Hauptkomponentenanalyse und dem Fisher-Yates Test werden Messdaten der Implementierung einer Ringoszillator PUF auf einem FPGA und der Implementierung einer Two-Stage PUF auf einem ASIC auf Schwachstellen hin untersucht. Hierbei werden auch die Vor- und Nachteile der zur Evaluierung verwendeten Verfahren beleuchtet. Die Ergebnisse zeigen, deutliche Nachteile bei der FPGA-Implementierung der Ringoszillator PUF, wahrend fur die Two-Stage PUF keine Schwachen identifiziert werden konnten.
SURF: Joint Structural Functional Attack on Logic Locking (2019)

To help protect hardware Intellectual Property (IP) blocks against piracy and reverse engineering, researchers have proposed various obfuscation techniques that aim at hiding design intent and making black-box usage difficult. A dominant form of obfuscation, referred to as logic locking, relies on the insertion of key gates (e.g., XOR/XNOR) at strategic locations in a design followed by logic synthesis. Recently, it has been shown that such an approach leaves predictable structural signatures, which make them susceptible to machine learning (ML) based structural attacks. These attacks are shown to deobfuscate a design by learning the deterministic nature of transformations incorporated by commercial synthesis tools. They are attractive for unraveling the design intent. However, they may not be able to provide a working design. In this paper, we introduce a novel attack on obfuscation techniques, called Structural Functional (SURF) attack, which, for the first time to our knowledge, accomplishes key extraction through scalable functional analysis while leveraging the output of structural attacks. We have developed complete flow and an automatic tool for the attack, which shows promising results. We are able to retrieve, on average, ~90% keybits for obfuscated ISCAS-85 benchmarks (100% in several cases) with > 98% output accuracy. We observe that SURF attack, unlike any known attack, can enable both discovering design intent as well as black-box usage. It is effective for all major variants of logic locking; scalable to large designs; and unlike SAT based attacks, is effective for all design types (e.g., multipliers, where SAT based attacks typically fail).
Optimal Trajectory for Curvature-Constrained UAV Mobile Base Stations (2020)

A set of optimal curvature-constrained closed trajectories for N unmanned aerial vehicle (UAV) mobile base stations (MBSs) supporting K ground terminals (GTs) is explored, which maximizes the minimum received signal strength (RSS) at the GT along its trajectory. It is proved that circular UAV maneuver turns out be optimal and the Euclidean N-center problem find the centers of the optimal circular trajectories. Numerical results demonstrate that optimized UAV trajectories improve the worst-case RSS by 100% compared to random UAV trajectories.
Topographic analysis of the S7 binding subsite of the tachykinin neurokinin‐1 receptor (1996)

Conformationally and configurationally restricted rotameric probes of phenylalanine have been incorporated in the sequence of substance P (SP)—Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH2—for analyzing the binding pockets of Phe7 (S7) and Phe8 (S8), in the neurokinin-1 receptor. These analogues of phenylalanine are (2S, 3R)- and (2S, 3S)-indanylglycines, E- and Z-α, β-dehydrophenylalanines, and 2(S)-α, β-cyclopropylphenylalanines [ΔE Phe, ΔZPhe, ▿E2(S)Phe, and ▿Z2(S)Phe]. Binding data obtained with either conformationally (Ing diastereoisomers) or configurationally (ΔEPhe, ΔZPhe) probes have unveiled large differences in the binding potencies of these rotameric probes. With the support of nmr data and energy calculations done on these SP-substituted analogues, we attempt to answer questions inherent to such study. First, none of these six probes prevents the formation of bioactive conformation(s) of the backbone of SP. Second, both diastereoisomers (S, S) and (S, R) of indanylglycine preferentially adopt, in the sequence of SP, the gauche (−) and trans side-chain orientations, respectively, as previously postulated from energy calculations with model peptides. However, in solution, the difference in energy between these rotamers included in the sequence of SP, compared to model peptides, is smaller since the other rotamer can be detected in [(2S, 3R) Ing7]SP. Finally, from this study we can hypothesize that the large variations observed in the affinities of Phe7 substituted analogues of SP must come from steric hindrance in the S7 binding site, which drastically restricts the space filling around the Cα (SINGLE BOND) Cβ bond of residue 7. © 1996 John Wiley & Sons, Inc.
Phage Therapy as an Alternative Treatment Modality for Resistant Staphylococcus aureus Infections (2023)

The production and use of antibiotics increased significantly after the Second World War due to their effectiveness against bacterial infections. However, bacterial resistance also emerged and has now become an important global issue. Those most in need are typically high-risk and include individuals who experience burns and other wounds, as well as those with pulmonary infections caused by antibiotic-resistant bacteria, such as <i>Pseudomonas aeruginosa</i>, <i>Acinetobacter sp,</i> and <i>Staphylococci</i>. With investment to develop new antibiotics waning, finding and developing alternative therapeutic strategies to tackle this issue is imperative. One option remerging in popularity is bacteriophage (phage) therapy. This review focuses on <i>Staphylococcus aureus</i> and how it has developed resistance to antibiotics. It also discusses the potential of phage therapy in this setting and its appropriateness in high-risk people, such as those with cystic fibrosis, where it typically forms a biofilm.
Encoding of natural scene statistics in the primary visual cortex of the mouse (2013)

The visual system has evolved to process ecologically relevant information in the organism’s natural environment, and thus it is believed to have adapted to its statistical properties. The most informative components of natural stimuli lie in their higher order statistical structure. If the primary visual cortex has indeed adapted to this higher order structure — as has been posited by theoretical studies over the last 20 years — neural responses to stimuli which differ in their statistical structure from natural scenes should exhibit pronounced deviations from responses to natural scenes. Theoretical studies argue for a sparse code for natural scenes, where only a few neurons need to be active simultaneously in order to encode visual information. However, it has been difficult to assess the sparseness of the neural representation directly and measure the ‘population sparseness’ in neural populations. Here we use 3D random access and conventional 2D two-photon imaging in mice to record populations of hundreds of neurons while presenting natural movies and movies where the higher order structure had been removed (phase scrambled). This technique allows assessing directly how sparse the representation of natural scenes in V1 really is and how this impacts the functional properties of the population code. First, we show that a decoder trying to discriminate between neural responses to different movie segments performs better for natural movies than for phase scrambled ones (nearest-neighbor classifier). Second, we show that this decoding accuracy improvement could be mainly explained through an increase in the sparseness of the neuronal representation. Finally, to explain the link between population sparseness and classification accuracy, we provide a simple geometrical interpretation. Our results demonstrate that the higher order correlations of natural scenes lead to a sparser neural representation in the primary visual cortex of mice and that this sparse representation improves the population read-out.
Immunization with genetically attenuated P52-deficient Plasmodium berghei sporozoites induces a long-lasting effector memory CD8+ T cell response in the liver (2011)

These results indicate that immunization of mice with P. berghei p52-GAP results in immune responses that are comparable to those induced by RAS or GAP lacking expression of UIS3 or UIS4, with an important role implicated for intrahepatic effector memory CD8+ T cells. The knowledge of the mediators of protective immunity after immunization with different GAP is important for the further development of vaccines consisting of genetically attenuated sporozoites.
Correction: Parkin ubiquitinates TAR-DNA binding protein-43 (TDP-43) and promotes its cytosolic accumulation via interaction with histone deacetylase 6 (HDAC6) (2022)

In the published article western blot image for Figure 4G HDAC6 panel was inserted by a mistake. The amended Figure 4G below shows the correct HDAC6 blot. The authors state that the scientific conclusions of the article are not affected by the correction.
Subharmonic hybrid mode-locking of a monolithic semiconductor laser (1996)

Performance of a subharmonically hybrid mode-locked (SH-ML) monolithic semiconductor laser is investigated. A 33-GHz passively mode-locked distributed Bragg reflector semiconductor laser is stabilized by the injection of an electrical signal with a subharmonic frequency of the laser cavity resonance. Systematic measurements on the phase noise, timing jitter, amplitude modulation, and locking bandwidth are performed for the second- and third-order SH-ML conditions, and the results are compared with the fundamental hybrid mode-locking (FH-ML) case. Low timing jitter of less than 0.6 ps, comparable to that under the FH-ML case, is achieved for the both SH-ML cases. The amplitude modulation imposed by the subharmonic driving frequencies is found to be very small (<-24 dBc) for the second-order SH-ML because of the sufficiently low modulation response of the laser at 16.5 GHz. The third-order SH-ML is found to exhibit a very unique locking characteristics, leading to a maximum locking bandwidth of 56 MHz that is even larger than that for the FH-ML case.
A Novel Inorganic Substrate by Three Dimensionally Stacked Glass Core Technology (2018)

2.5D and 2.1D technologies aim at improving wiring density and packaging density. However, both 2.5D and 2.1D technologies present coefficient of thermal expansion (CTE) mismatch issues and an increase in the assembly process. To overcome such limitations, we developed a glass package stacked glass core which uses the conductive paste as interlayer connection vias. We fabricated and then studied a multilayer glass package substrate. The daisy chain of such multilayer glass package substrate passed through a reflow test for five times. During the reflow process, the warpage of the multilayer glass package substrate turns to be lower than that of an organic package substrate. In addition, the CTE of the multilayer glass package substrate is approximately 3 ppm/°C, as in silicon. The bending strain of the multilayer glass package substrate becomes stronger as the number of layers increase and its internal stress is lower than the glass interposer. We believe that the proposed multilayer glass package substrate will guarantee high-density wiring, with high reliability and high packaging density, and that it can be optimally used in practical applications instead of 2.5D and 2.1D technology.
Measurement of the correlation between flow harmonics of different order in lead-lead collisions at sNN=2.76 TeV with the ATLAS detector (2015)

Correlations between the elliptic or triangular flow coefficients v m (m = 2 or 3) and other flow harmonics v n (n = 2 to 5) are measured using s NN = 2.76 TeV Pb + Pb collision data collected in 2010 by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 7 b -1 . The v m -v n correlations are measured in midrapidity as a function of centrality, and, for events within the same centrality interval, as a function of event ellipticity or triangularity defined in a forward rapidity region. For events within the same centrality interval, v 3 is found to be anticorrelated with v 2 and this anticorrelation is consistent with similar anticorrelations between the corresponding eccentricities, 2 and 3 . However, it is observed that v 4 increases strongly with v 2 , and v 5 increases strongly with both v 2 and v 3 . The trend and strength of the v m -v n correlations for n = 4 and 5 are found to disagree with mn correlations predicted by initial-geometry models. Instead, these correlations are found to be consistent with the combined effects of a linear contribution to v n and a nonlinear term that is a function of v 2 2 or of v 2 v 3 , as predicted by hydrodynamic models. A simple two-component fit is used to separate these two contributions. The extracted linear and nonlinear contributions to v 4 and v 5 are found to be consistent with previously measured event-plane correlations.
27‐3: High Performance Fringe Field Switching Mode Liquid Crystal Display with Photo‐alignment Technology for Vehicular Application (2018)

We have developed a novel photo‐alignment FFS‐LCD (PA‐FFS‐LCD) with a wide nematic temperature range from ‐40°C to 95°C. Our developed PA‐FFS‐LCD shows fast gray‐to‐gray response time (&lt; 20 ms at 25°C and &lt; 300 ms at ‐30°C), wide viewing angle, and high contrast ratio over 1500. Image sticking was not recognized owing to a suitable configuration of pixel and common electrodes. The developed LCD can be used for vehicular application.
Molecular prediction of patient prognosis. (2009)

Each cancer is unique: it reflects the underlying genetic make-up of the patient and the stochastic mutational processes that occur within the tumour. This uniqueness suggests that each patient should receive a personalized type of therapy. Current predictions of a cancer patient’s outcome or prognosis are highly inaccurate. To aid in the prediction of patient prognosis based on highthroughput molecular datasets I have worked to optimize each step of the experimental pipeline: platform annotation, experimental design, consideration of tumour heterogeneity, data pre-processing and statistical analysis, and feature selection. First, a 12k CpG Island clone library was sequenced and annotated using a BLAT analysis. Second, microarrays built using this library were used in a fully-saturated study to evaluate the importance of ChIP-chip experimental design parameters. Third, intra-tumour heterogeneity was shown to influence specific pathways in a large fraction of genes. Fourth, a systematic empirical evaluation of 19,446 combinations of microarray analysis methods identified key steps of the analysis process and provided insight into their optimization. Finally, the combination of a two-stage experimental design and a novel semi-supervised algorithm yielded a six-gene, mRNA abundance-based classifier that could divide non-small cell lung cancer patients into two groups with significantly different outcomes in four independent validation cohorts. Further, a permutation study showed that millions of six-gene markers exist, but that ours ranked amongst the top 99.98% of all six-gene markers. The knowledge gained from these studies provides a key foundation for the development of personalized therapies for cancer patients.
Carbon Nanotube‐Epoxy Nanocomposites: Correlation and Integration of Dynamic Impedance, Dielectric, and Mechanical Analyses (2013)

This study focuses on the characterization of MWNT‐epoxy composites for different MWNT concentrations of 0–7 wt% by correlating different dynamic analysis techniques, including DMA, impedance, and DEA. An optimum composition was established at 0.1 wt% MWNTs corresponding to the best MWNT dispersion which resulted in the formation of an optimum MWNT network. The addition of this low fraction of MWNTs in epoxy resulted in stiffening the molecular structure and suppressing certain molecular transitions, raising the dielectric constant especially in the low‐to‐medium frequency range, raising the electrical conductivity especially at the high frequencies, and increasing the electromagnetic shielding effectiveness. The 0.1% MWNT‐epoxy nanocomposite switched the electromagnetic shielding behaviour from being a very effective absorber at low frequencies to being an effective reflector at high frequencies. Finally, the Nyquist plot derived from the dynamic impedance spectroscopy proved most useful at providing evidence of multiple size distribution of MWNT agglomerates.
Regulation of bone remodeling by vasopressin explains the bone loss in hyponatremia (2013)

Although hyponatremia is known to be associated with osteoporosis and a high fracture risk, the mechanism through which bone loss ensues has remained unclear. As hyponatremic patients have elevated circulating arginine-vasopressin (AVP) levels, we examined whether AVP can affect the skeleton directly as yet another component of the pituitary-bone axis. Here, we report that the two Avp receptors, Avpr1α and Avpr2, coupled to Erk activation, are expressed in osteoblasts and osteoclasts. AVP injected into wild-type mice enhanced and reduced, respectively, the formation of bone-resorbing osteoclasts and bone-forming osteoblasts. Conversely, the exposure of osteoblast precursors to Avpr1α or Avpr2 antagonists, namely SR49059 or ADAM, increased osteoblastogenesis, as did the genetic deletion of Avpr1α. In contrast, osteoclast formation and bone resorption were both reduced in Avpr1α(-/-) cultures. This process increased bone formation and reduced resorption resulted in a profound enhancement of bone mass in Avpr1α(-/-) mice and in wild-type mice injected with SR49059. Collectively, the data not only establish a primary role for Avp signaling in bone mass regulation, but also call for further studies on the skeletal actions of Avpr inhibitors used commonly in hyponatremic patients.