gebhart/patrepeval huggingface dataset:
Mechanical Search on Shelves with Efficient Stacking and Destacking of Objects (2022)

Stacking increases storage efficiency in shelves, but the lack of visibility and accessibility makes the mechanical search problem of revealing and extracting target objects difficult for robots. In this paper, we extend the lateral-access mechanical search problem to shelves with stacked items and introduce two novel policies -- Distribution Area Reduction for Stacked Scenes (DARSS) and Monte Carlo Tree Search for Stacked Scenes (MCTSSS) -- that use destacking and restacking actions. MCTSSS improves on prior lookahead policies by considering future states after each potential action. Experiments in 1200 simulated and 18 physical trials with a Fetch robot equipped with a blade and suction cup suggest that destacking and restacking actions can reveal the target object with 82--100% success in simulation and 66--100% in physical experiments, and are critical for searching densely packed shelves. In the simulation experiments, both policies outperform a baseline and achieve similar success rates but take more steps compared with an oracle policy that has full state information. In simulation and physical experiments, DARSS outperforms MCTSSS in median number of steps to reveal the target, but MCTSSS has a higher success rate in physical experiments, suggesting robustness to perception noise. See https://sites.google.com/berkeley.edu/stax-ray for supplementary material.
Intrinsic Fluorescence Spectroscopy of Biological Tissue (2003)

This chapter describes intrinsic fluorescence spectroscopy (IFS), a method for recovering of the intrinsic tissue fluorescence from the measured fluorescence, using the diffuse reflectance collected at the same site with the same probe. It demonstrates the validity of this model over a wide range of scattering and absorption coefficients with experiments performed using physical tissue models and ex vivo tissues. The chapter utilizes IFS to determine in vivo the intrinsic tissue fluorescence spectra of collagen and the reduced form of nicotinamide adenine dinucleotide, the two major tissue chromophores for excitation in the 337- to 425-nm range. Fluorescence recorded from a turbid medium such as biological tissue contains information not only about the fluorescence of individual fluorophores but also about scattering and absorption. In photon migration theory, light propagation in a turbid medium is described in terms of photons traveling in paths with discrete photon-tissue interaction events of absorption, scattering, and fluorescence.
Image Contrast Of Amorphous Carbonaceous Materials (1977)

We have previously reported a method for preparing extremely thin films of graphite single crystals for use as support films (1). Usefulness of these films, in particular, for obtaining high resolution images of phase objects, was demonstrated by imaging (with bright field mode of CTEM) surface steps with heights of less than 10Å on graphite films (2) and also single atoms of tungsten (3). In this study using the same graphite substrates we have made some observations of amorphous materials to understand the image contrasts in terms of microstructure. Although image contrasts of thin evaporated carbon films, even if prepared as thin as possible, do not show measurable dependence on film thicknesses, we chose as test objects the extremely thin films of contamination which grew discontinuously on the substrate films during specimen observation (4). Image contrasts of these films were then compared with those of known structures such as surface steps and a single layer of graphite crystal.
Diffraction efficiency optimization for multilayered parametric holographic gratings (2021)

Multilayered diffraction gratings are an essential component in many optical devices due to their ability to engineer light. We propose a first-order optimization strategy to maximize diffraction efficiencies of such structures by a fast approximation of the underlying boundary integral equations for polarized electromagnetic fields. A parametric representation of the structure interfaces via trigonometric functions enables the problem to be set as a parametric optimization one while efficiently representing complex structures. Derivatives of the efficiencies with respect to geometrical parameters are computed using shape calculus, allowing a straightforward implementation of gradient descent methods. Examples of the proposed strategy in chirped pulse amplification show its efficacy in designing multilayered gratings to maximize their diffraction efficiency.
Impaired Regulation by IL-35 in Systemic Sclerosis (2023)

This study investigated the role of IL-35 in systemic sclerosis (SSc) patients, focusing on CD4+ T cell response and immunomodulatory cytokine production. By comparing the cytokine levels in healthy donors (HD) and SSc patients using ELISAs, we found a significantly lower plasma IL-35 concentration in the SSc patients (52.1 ± 5.6 vs. 143 ± 11.1, <i>p</i> < 0.001). Notably, the IL-35 levels showed a negative correlation with TGF-β (<i>p</i> < 0.001) and IL-17 (<i>p</i> = 0.04). Assessing the IL-35R expression across cell types in the SSc patients and HDs via flow cytometry, we found higher levels on monocytes (40.7 + 5.7 vs. 20.3 ± 1.9, <i>p</i> < 0.001) and lower levels on CD8+ T cells (61.8 ± 9.2 vs. 83.4 ± 0.8, <i>p</i> < 0.05) in the SSc patients. The addition of recombinant IL-35 to stimulated peripheral blood mononuclear cells reduced the IL-17+CD4+ T cell percentage (9.0 ± 1.5 vs. 4.8 ± 0.7, <i>p</i> < 0.05) and increased the IL-35+CD4+ T percentage (4.1 ± 2.3 vs. 10.2 ± 0.8, <i>p</i> < 0.001). In a Treg:Tresponder cell Sco-culture assay with HD and SSc samples, rIL35 decreased the cell proliferation and levels of IL-17A (178.2 ± 30.5 pg/mL vs. 37.4 ± 6.4 pg/mL, <i>p</i> < 0.001) and TGF-β (4194 ± 777 pg/mL vs. 2413 ± 608 pg/mL, <i>p</i> < 0.01). Furthermore, we observed a positive correlation between the modified Rodnan skin score (mRSS) and TGF-β (<i>p</i> < 0.001), while there was a negative correlation between mRSS and IL-35 (<i>p</i> = 0.004). Interestingly, higher levels of plasmatic IL-35 were detected in individuals with limited disease compared to those with diffuse disease (60.1 ± 8.0 vs. 832.3 ± 4.1, <i>p</i> < 0.05). These findings suggest that IL-35 exhibits anti-inflammatory properties in SSc and it may serve as a marker for disease severity and a therapeutic target.
A uniform architecture for parsing and generation (1988)

The use of a single grammar for both parsing and generation is an idea with a certain elegance, the desirability of which several researchers have noted. In this paper, we discuss a more radical possibility: not only can a single grammar be used by different processes engaged in various "directions" of processing, but one and the same language-processing architecture can be used for processing the grammar in the various modes. In particular, parsing and generation can be viewed as two processes engaged in by a single parameterized theorem prover for the logical interpretation of the formalism. We discuss our current implementation of such an architecture, which is parameterized in such a way that it can be used for either purpose with grammars written in the PATR formalism. Furthermore, the architecture allows fine tuning to reflect different processing strategies, including parsing models intended to mimic psycholinguistic phenomena. This tuning allows the parsing system to operate within the same realm of efficiency as previous architectures for parsing alone, but with much greater flexibility for engaging in other processing regimes.
The Telomere Length Landscape of Prostate Cancer (2021)

Abstract Replicative immortality is a hallmark of cancer, and can be achieved through telomere lengthening and maintenance. We report telomere lengths (TLs) of 392 localized prostate cancer tumours and characterize their relationship to genomic, transcriptomic and proteomic features. Shorter tumour TLs were associated with elevated genomic instability, including single-nucleotide variants, indels and structural variants. Genes involved in cell proliferation and signaling were correlated with tumour TL at all levels of the central dogma. TL was also associated with multiple clinical features of a tumour. Longer TLs in non-tumour samples were associated with a lower rate of biochemical relapse after definitive local therapy. Our analysis integrates multi-omics data to illuminate the relationship of specific genomic alterations in a tumour and TL in prostate cancer. Although the role of telomere length in cancer has been well studied, its association to genomic features is less well known. We describe the multi-level integration of telomere length, genomics, transcriptomics and proteomics in localized prostate cancer. Patient Summary We examined the association between telomere length and multiple omics-level data in prostate cancer. We observed that traditional telomere mutations are rare in prostate cancer and that telomere length is associated with multiple measure of genomic instability.
Digitally Optimized Delta-Sigma Modulator for WiMAX Transmitter Design (2007)

International audience
Abstract SY34-01: Biomarkers for predicting response to PI3K inhibitors (2011)

Abstract Phosphoinositide 3-kinase (PI 3-kinase) is a central enzyme in a signaling pathway that mediates cellular responses to growth factors. The pathway is highly conserved from worms and flies to humans and genetic analysis of the pathway has revealed a conserved role in regulating glucose metabolism, cell growth and organism longevity. Based on deletion of genes encoding the catalytic or regulatory subunits of PI 3-kinase in the mouse, PI 3-kinase mediates insulin-dependent regulation of glucose metabolism, and defects in activation of this pathway result in insulin resistance and type 2 diabetes. In contrast, mutational events that lead to hyperactivation of PI 3-kinase result in cancers. Activating mutations in PIK3CA, encoding the p110alpha catalytic subunit of PI 3-kinase or inactivating mutations in PTEN, a phosphoinositide 3-phosphatases that reverses the effects of PI 3-kinase, are among the most common events in solid tumors. We, and others have generated mouse models in which a mutated form of the PIK3CA gene is expressed in a tissue-specific and reversibly inducible manner. These mice develop cancers that are dependent on continuous expression of the mutant PIK3CA gene. The PIK3CA driven tumors are FDG-PET positive and turning off PI 3-kinase with drugs results in an acute decline in FDG-PET signal that precedes tumor shrinkage. These results suggest that the ability of PI 3-kinase to stimulate high rates of glucose uptake and metabolism may be critical for the survival of PIK3CA mutant tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr SY34-01. doi:10.1158/1538-7445.AM2011-SY34-01
Isolation and characterization of recombinant DNA clones of avian retroviruses: size heterogeneity and instability of the direct repeat (1980)

Unintegrated proviral DNA of Schmidt-Ruppin B Rous sarcoma virus was cloned in the bacteriophage lambda vector Charon 21A. A total of 12 independent recombinant lambda SRBtd clones which were derived from the transformation-defective component in the viral preparation were analyzed with restriction endonucleases and molecular hybridization techniques. Three classes of clones were observed. Type I clones contained a 5.0-megadalton insert of viral DNA, type II clones contained phage with two size classes of inserts (5.0 and 5.2 megadaltons), and one type III clone contained only a 5.2-megadalton insert. The smaller insert present in type II clones appeared to be derived by deletion of one copy of a directly repeated sequence which was present in the larger insert. Mapping data indicated that the deletion includes all or part of the terminal repeat found in linear double-stranded proviral DNA. Similar results were obtained from lambda RAV2 recombinant clones derived from Rous-associated virus type 2. Analysis of DNA from type II and type III clones of lambda SRBtd and lambda RAV2 revealed limited heterogeneity in the size of the direct repeat.
Base‐Free Iron Catalyzed Transfer Hydrogenation of Esters Using EtOH as Hydrogen Source (2018)

Abstract Herein, we report on the use of the iron pincer complex Iron‐MACHO‐BH, in the base‐free transfer hydrogenation of esters with EtOH as a hydrogen source. More than 20 substrates including aromatic and aliphatic esters and lactones were reduced affording the desired primary alcohols and diols with moderate to excellent isolated yields. It is also possible to reduce polyesters to the diols with this method, enabling a novel way of plastic recycling. Reduction of the renewable substrate methyl levulinate proceeds to form 1,4‐pentanediol directly. The yields are largely governed by the equilibrium between the alcohol and the ethyl ester.
Deformable registration of CT and cone-beam CT by local CBCT intensity correction (2015)

In this paper, we propose a method to accurately register CT to cone-beam CT (CBCT) by iteratively correcting local CBCT intensity. CBCT is a widely used intra-operative imaging modality in image-guided radiotherapy and surgery. A short scan followed by a filtered-backprojection is typically used for CBCT reconstruction. While data on the mid-plane (plane of source-detector rotation) is complete, off-mid-planes undergo different information deficiency and the computed reconstructions are approximate. This causes different reconstruction artifacts at off-mid-planes depending on slice locations, and therefore impedes accurate registration between CT and CBCT. To address this issue, we correct CBCT intensities by matching local intensity histograms slice by slice in conjunction with intensity-based deformable registration. This correction-registration step is repeated until the result image converges. We tested the proposed method on eight head-and-neck cancer cases and compared its performance with state-of-the-art registration methods, Bspline, demons, and optical flow, which are widely used for CT-CBCT registration. Normalized mutual-information (NMI), normalized cross-correlation (NCC), and structural similarity (SSIM) were computed as similarity measures for the performance evaluation. Our method produced overall NMI of 0.59, NCC of 0.96, and SSIM of 0.93, outperforming existing methods by 3.6%, 2.4%, and 2.8% in terms of NMI, NCC, and SSIM scores, respectively. Experimental results show that our method is more consistent and roust than existing algorithms, and also computationally efficient with faster convergence.
Effects of nasal CPAP therapy on respiratory and spontaneous arousals in infants with OSA (1999)

Obstructive sleep apnea (OSA) in infants has been shown to resolve frequently without a cortical arousal. It is unknown whether infants do not require arousal to terminate apneas or whether this is a consequence of the OSA. We studied the apnea and arousal patterns of eight infants with OSA before and after treatment with nasal continuous positive airway pressure (CPAP). These infants were age matched to eight untreated infants with OSA and eight normal infants. Polysomnographic studies were performed on each infant. We found that the majority of central and obstructive apneas were terminated without arousal in all OSA infants. After several weeks of nasal CPAP treatment, the proportion of apneas terminating with an arousal during rapid-eye-movement sleep increased in treated infants compared with untreated infants. Spontaneous arousals during rapid-eye-movement sleep were reduced in all OSA infants; however, during CPAP treatment, the spontaneous arousals increased to the normal control level. We conclude that OSA in infants possibly depresses the arousal response and treatment of these infants with nasal CPAP partially reverses this depression.
Supplementary Figure S3 from Genomic Instability and Protumoral Inflammation Are Associated with Primary Resistance to Anti–PD-1 + Antiangiogenesis in Malignant Pleural Mesothelioma (2023)

&lt;p&gt;Further descriptions of tumor immune infiltrates.&lt;/p&gt;
Single-Molecule Activation and Quantification of Mechanically Triggered Palladium–Carbene Bond Dissociation (2021)

Metal-complexed N-heterocyclic carbene (NHC) mechanophores are latent reactants and catalysts for a range of mechanically driven chemical responses, but mechanochemical scission of the metal-NHC bond has not been experimentally characterized. Here we report the single-molecule force spectroscopy of ligand dissociation from a pincer NHC-pyridine-NHC Pd(II) complex. The force-coupled rate constant for ligand dissociation reaches 50 s<sup>-1</sup> at forces of approximately 930 pN. Experimental and computational observations support a dissociative, rather than associative, mechanism of ligand displacement, with rate-limiting scission of the Pd-NHC bond followed by rapid dissociation of the pyridine moiety from Pd.
A double step synthesis of mesoporous micrometric spherical MSU-X silica particles (1999)

Spherical particles of mesoporous MSU-X silica in the micrometric size range have been obtained through a new double step process that led to an easy and highly reproducible synthesis pathway giving micelle templated structures with a large surface area and narrow pore size distribution
High Density Hybrid Switched Capacitor Converter for Data-Center Application (2021)

Data center electricity consumption has been rapidly increasing in the last few years as computation moves into cloud computing [1]. With the introduction of the 48 V power-delivery architecture a two-stage approach is commonly adopted where the regulation is established at second-stage level with an unregulated first stage. Typically the first stage is a fix ratio dc-dc converter, such as LLC or switching-capacitor converter. In this paper a novel unregulated non-isolated hybrid switched capacitor resonant converter is proposed for the first stage conversion from 48-V to 6-V. Experimental results for a 750W prototype in 8th brick form factor are showing the effectiveness of the proposed approach.
Synthesis and Anticancer Evaluation of New Indole-Based Tyrphostin Derivatives and Their (p-Cymene)dichloridoruthenium(II) Complexes (2023)

New <i>N</i>-alkylindole-substituted 2-(pyrid-3-yl)-acrylonitriles with putative kinase inhibitory activity and their (<i>p</i>-cymene)Ru(II) piano-stool complexes were prepared and tested for their antiproliferative efficacy in various cancer models. Some of the indole-based derivatives inhibited tumor cell proliferation at (sub-)micromolar concentrations with IC<sub>50</sub> values below those of the clinically relevant multikinase inhibitors gefitinib and sorafenib, which served as positive controls. A focus was set on the investigation of drug mechanisms in HCT-116 p53-knockout colon cancer cells in order to evaluate the dependence of the test compounds on p53. Colony formation assays as well as experiments with tumor spheroids confirmed the excellent antineoplastic efficacy of the new derivatives. Their mode of action included an induction of apoptotic caspase-3/7 activity and ROS formation, as well as anti-angiogenic properties. Docking calculations with EGFR and VEGFR-2 identified the two 3-aryl-2-(pyrid-3-yl)acrylonitrile derivatives <b>2a</b> and <b>2b</b> as potential kinase inhibitors with a preferential activity against the VEGFR-2 tyrosine kinase. Forthcoming studies will further unveil the underlying mode of action of the promising new derivatives as well as their suitability as an urgently needed novel approach in cancer treatment.
Pharmacokinetics and safety of paclitaxel delivery into porcine airway walls by a new endobronchial drug delivery catheter (2017)

Results of these studies confirm the administration of PTX directly into the bronchial wall is safe and feasible. PTX was detectable in plasma for <7 days but tissue concentrations remained therapeutic throughout the follow-up period.
Integrating Rock Physics, 4D Inversion and Time-Shifts for Pressure and Waterflooding Discrimination in Jubarte Field (Brazil) (2020)

Summary The use of 4D quantitative interpretations in the characterization of oil reservoirs is essential for reservoir management, once it reduces ambiguities and facilitates the incorporation of information for history-matching. This work is a 4D quantitative interpretation focusing on the post-salt reservoir of Jubarte field, a Brazilian deep-water oil field. In this project, we face the challenge of conducting a 4D study using acquisitions only one year apart, which was overcome by using a permanent reservoir monitoring system (PRM). We present an integrated interpretation of 4D elastic inversion and time-shifts volumes, taking as reference a calibrated rock physics model. Given the differential sensitivity of these properties to changes in reservoir fluid pressure and saturation, they can be used to infer effects that are fundamental to decision making involving reservoir management.
Branch and bound methods based tone injection schemes for PAPR reduction of DCO-OFDM visible light communications (2017)

In this paper, the peak-to-average power ratio (PAPR) reduction problem with tone injection (TI) in the direct current-biased optical orthogonal frequency division multiplexing (DCO-OFDM) system is investigated, which is formulated as a tough integer combinatorial optimization problem. Since it is a challenging task to find the global optimal solution, the branch-and-bound method (BBM), which is extensively employed to deal with the NP-hard problem, is introduced to solve this problem. By splitting the superior branches and pruning the inferior branches, the close optimal solution is obtained. Simulation results reveal that the proposed BBM-based TI method has superior PAPR reduction and bit error rate (BER) performance compared with some existing algorithms. The proposed algorithm ensures a relatively low peak value, and thus provides an important benchmark in performance evaluations relative to other existing algorithms targeting at the same problem.
Effects of Rat Hepatocytes on Macromolecular Permeability of Bovine Aortic Endothelial Cell Monolayer (1996)

The aim of this study was to examine whether the hyperpermeable structure of the liver endothelium in vivo is related to the interactions of hepatocytes in a culture system. The permeation of macromolecular FITC-labeled dextran (molecular weight 70,000) through a monolayer of bovine aortic endothelial cells (BAEC), cocultured with rat parenchymal hepatocytes (P-hep), was increased. When the BAEC were cocultured with nonparenchymal hepatocytes (N-hep), the permeability of the BAEC monolayer was not increased. However, when the BAEC were cocultured with a mixture of P-hep and N-hep (PN-hep), the BAEC monolayer was more permeable than when BAEC were cocultured with P-hep alone. The conditioned medium of P-hep did not alter the BAEC monolayer permeability, nor did the extracellular matrix of P-hep alter BAEC permeability. When the BAEC were cocultured with PN-hep, the F-actin content was not altered. These findings suggest that the interaction between hepatocytes and endothelial cells exerts an important effect on the hyperpermeable structure of the liver vessels in vivo.
Factors influencing the water proton relaxation in nuclear fractions from tissues of normal and tumor-bearing animals. (1982)

Water proton spin-lattice relaxation times (T1) were measured in nuclear fractions from liver, kidney, and spleen tissues from normal and tumor-bearing animals (TBA) at two frequencies. At 9 MHz, the T1 values for TBA nuclear fractions are less than those for normal nuclear fractions, contrary to observations at the cellular level. Trace metal ion concentration and nucleic acid content estimated for these nuclear fractions suggest that the DNA-metal ion interaction might be responsible for the observed differences in the T1 of nuclear fractions at low frequencies.