gebhart/patrepeval huggingface dataset:
Immunocytochemical Localization of Sex Steroid Hormone Receptors in Normal Human Mammary Gland (2009)

The sex steroids, estrogens, progesterone, and androgens, all play a role in mammary development and function. To precisely identify the sites of action of these steroids, we studied the localization of the estrogen receptor alpha (ERalpha) and ERbeta, the progesterone receptor A (PRA) and PRB, and androgen receptors (AR) in the normal human mammary gland. Immunocytochemical localization of ERalpha, ERbeta, PRA, PRB, and AR was performed with reduction mammoplasty specimens from premenopausal women. ERalpha, PRA, PRB, and AR were localized mostly to the inner layer of epithelial cells lining acini and intralobular ducts, as well as to myoepithelial cells scattered in the external layer of interlobular ducts. AR was also found in some stromal cells. ERbeta staining was more widespread, resulting in epithelial and myoepithelial cells being labeled in acini and ducts as well as stromal cells. These results suggest that all sex steroids can directly act on epithelial cells to modulate development and function of the human mammary gland. Estrogens and androgens can also indirectly influence epithelial cell activity by an action on stromal cells.
Retinal Identification System based on Optical Disc Ring Extraction and New Local SIFT-RUK Descriptor (2018)

International audience
Strong Reduction in Ge Film Reflectivity by an Overlayer of 3 nm Si Nanoparticles: Implications for Photovoltaics (2021)

We examine the effect of a top nanofilm of 3 nm silicon nanoparticles (Si-NPs) on the spectral features of the reflectivity of germanium (Ge). We use a 450 nm Ge layer grown by low temperature plasma enhanced chemical vapor deposition on a crystalline Si substrate. The Si-NPs are drop casted incrementally on the Ge/Si structure from a particle colloid, forming a nanofilm of increasing thickness up to 30 nm. The stack is characterized using luminescence microscopy, atomic force microscopy, transmission electron microscopy, and reflectivity spectroscopy. The reflectance of the stack is measured over UV/visible and infrared range 4.8–0.8 eV. With the increasing thickness of the Si nanocoating, the results show a strong reduction in the reflectivity of Ge in the visible and blue-UV region of the spectrum with less effect in the infrared, as well as a difference in reflectance at the adjacent lying complex of Λ and L transitions of Ge. The strong reduction in the visible/UV range is understood in terms of a near overlap of the band to band transitions of Si-NPs and Ge. The diminished response in the infrared contributes to shifting of the bandgap of Si-NPs from the infrared to the visible due to quantum confinement. Furthermore, optical properties of Si-NP are estimated and samples are analyzed using Modified Transfer Matrix Method model. The strong reduction of reflectivity of Ge in the visible-UV region is very useful in photovoltaics, with special emphasis on Ge-based multijunction solar cells.
Surgical salvage of human papillomavirus–positive oropharyngeal cancer: Secondary analysis of a randomized controlled trial (2022)

Salvage surgery in patients with HPV+ OPSCC is associated with favorable survival and adverse event outcomes.
Enantioselective Synthesis of Functionalized 1,5-Cyclononadienes by Intramolecular Cycloalkylation under alpha,alpha'-Diallyl Coupling This work was supported by the Deutsche Forschungsgemeinschaft (Sonderforschungsbereich 424) and the Fonds der Chemischen Industrie. A.D. gratefully acknowledges a fellowship from the Fonds der Chemischen Industrie. We thank Mrs. C. Weitkamp for her outstanding experimental assistance and Mr. J. Müller for his skillful work during a laboratory course. (2000)

Monocarbocyclic nine-membered rings can be enantioselectively accessed by deprotonation of (Z,Z)-dienyl carbamates 1 and subsequent intramolecular α,α′-coupling to furnish the cyclononadienols 2 (R=H: 73% yield, e.r.=96:4; R=OSiPh2tBu: 79% yield, e.r.=100:0, d.r.=94:6). Cby=2,2,4,4-Tetramethyl-1,3-oxazolidin-3-ylcarbonyl, Cb=diisopropylaminocarbonyl.
Development and MASH Full-Scale Crash Testing of a High-Mounting-Height Temporary Single Sign Support with Aluminum Sign (2013)

Work zone traffic control devices such as temporary single sign supports are a primary means to communicate information to motorists in work zone areas. The Federal Highway Administration and the Manual on Uniform Traffic Control Devices require work zone traffic control devices to be crashworthy. That is, they should not pose a safety hazard to motorists and/or work zone personnel if impacted by errant vehicles. The objective of this research was to develop a nonproprietary, lightweight, crashworthy, work-zone single sign support for use with an aluminum sign substrate mounted at a height of 7 ft. The device is intended to meet the evaluation criteria in the American Association of State Highway and Transportation Officials (AASHTO) Manual for Assessing Safety Hardware (MASH). Texas A&M Transportation Institute (TTI) researchers decided to utilize perforated steel tubing for the frame of the new temporary single sign support system to accommodate requests to help make the system lightweight, durable, easy to assemble, and adjustable. Design concepts were developed and evaluated through engineering analysis, developmental full-scale crash tests, and finite element computer simulations. Results were reviewed with the project monitoring committee and a system was selected by Texas Department of Transportation (TxDOT) for evaluation through full-scale crash testing. MASH Test 3-72 with the 2270P pickup truck was performed to evaluate the behavior of the sign support oriented at both 90 degrees and 0 degrees. The sign support system oriented at 0 degrees passed all the MASH evaluation criteria. Secondary contact between the pickup truck and the aluminum sign panel of the sign support system oriented at 90 degrees caused a cut in the roof that constituted occupant compartment intrusion. Consequently, the sign support system did not pass MASH occupant risk criteria. The report recommendations possible design modifications to mitigate this behavior and improve impact performance for the pickup truck.
Mechanical Search on Shelves using Lateral Access X-RAY (2020)

Efficiently finding an occluded object with lateral access arises in many contexts such as warehouses, retail, healthcare, shipping, and homes. We introduce LAX-RAY (Lateral Access maXimal Reduction of occupancY support Area), a system to automate the mechanical search for occluded objects on shelves. For such lateral access environments, LAX-RAY couples a perception pipeline predicting a target object occupancy support distribution with a mechanical search policy that sequentially selects occluding objects to push to the side to reveal the target as efficiently as possible. Within the context of extruded polygonal objects and a stationary target with a known aspect ratio, we explore three lateral access search policies: Distribution Area Reduction (DAR), Distribution Entropy Reduction (DER), and Distribution Entropy Reduction over Multiple Time Steps (DER-MT) utilizing the support distribution and prior information. We evaluate these policies using the First-Order Shelf Simulator (FOSS) in which we simulate 800 random shelf environments of varying difficulty, and in a physical shelf environment with a Fetch robot and an embedded PrimeSense RGBD Camera. Average simulation results of 87.3% success rate demonstrate better performance of DER-MT with 2 prediction steps. When deployed on the robot, results show a success rate of at least 80% for all policies, suggesting that LAX-RAY can efficiently reveal the target object in reality. Both results show significantly better performance of the three proposed policies compared to a baseline policy with uniform probability distribution assumption in non-trivial cases, showing the importance of distribution prediction. Code, videos, and supplementary material can be found at https://sites.google.com/berkeley.edu/lax-ray.
APEX (2010)

The changing nature of document workflows, document privacy and document security merit a new approach to the enforcement of policy. We propose the use of automated means for enforcing policy, which provides advantages for compliance and auditing, adaptability to changes in policy, and compatibility with a cloud-based exchange. We describe the Automated Policy Enforcement eXchange (APEX) software system, which consists of: (1) a policy editor, (2) a policy server, (3) a local daemon on every PC/laptop to maintain local secure up-to-date storage and policy, and (4) local (policy-enforcing) wrappers to capture document-handling user actions such as document export, e-mail, print, edit and save. During the performance of relevant incremental change, or other user-elicited action, on a composite document, the document and its metadata are scanned for salient policy eliciting terms (PETs). The document is then partitioned based on relevant policies and the security policy for each part is determined. If the document contains no PETs, then the user-initiated actions are allowed; otherwise, alternative actions are suggested, including: (a) encryption, (b) redirecting to a secure printer and requiring authorization (e.g. PIN) for printing, and (c) disallowing printing until specific sensitive data is removed.
Skeletal muscle contraction in protecting joints and bones by absorbing mechanical impacts (2016)

We have previously hypothesized that the dissipation of mechanical energy of external impact is a fundamental function of skeletal muscle in addition to its primary function to convert chemical energy into mechanical energy. In this paper, a mathematical justification of this hypothesis is presented. First, a simple mechanical model, in which the muscle is considered as a simple Hookean spring, is considered. This analysis serves as an introduction to the consideration of a biomechanical model taking into account the molecular mechanism of muscle contraction, kinetics of myosin bridges, sarcomere dynamics, and tension of muscle fibers. It is shown that a muscle behaves like a nonlinear and adaptive spring tempering the force of impact and increasing the duration of the collision. The temporal profiles of muscle reaction to the impact as functions of the levels of muscle contraction, durations of the impact front, and the time constants of myosin bridges closing, are obtained. The absorption of mechanical shock energy is achieved due to the increased viscoelasticity of the contracting skeletal muscle. Controlling the contraction level allows for the optimization of the stiffness and viscosity of the muscle necessary for the protection of the joints and bones.
ELECTRODE DESIGN OPTIMIZATION FOR IMPROVED LITHIUMION CELL LONGEVITY IN IMPLANTABLE APPLICATIONS (2003)

Purpose: Many medical devices require an implantable power source. For devices with high energy requirements, a rechargeable power source may be required. Lithium-ion batteries have been proposed for these applications due to their high energy density, low self-discharge, excellent safety and long cycle life. Because of the issues surrounding replacement of implanted batteries, it is critical that acceptable battery lifetimes are achieved. We studied the effect of electrode design on the longevity of lithium-ion batteries in demanding implantable applications in order to optimize performance. Methods: Batteries were designed, built, and tested using a design of experiments approach (2 factors, 3 levels). The experimental factors used were electrode loading and anode density. The test groups were evaluated to determine cycle life and capacity retention during battery storage. All testing was done at 37°C to simulate internal body temperature. Results: Battery capacity and runtime at beginning-of-life was shown to be favored by high anode density and high electrode loading. However, batteries were shown to have better cycle life and storage properties at lower electrode loadings. Cycle life and storage properties were also favored by high anode density, however, the impact of anode density was reduced with decreasing electrode loading. This knowledge allows optimization of longevity and runtime for a specific application.
Cationic polymerization of norbornadiene (2003)

Abstract The polymerization of norbornadiene (NBD) initiated by the 2‐chloro‐2,4,4‐trimethylpentane/titanium tetrachloride system was investigated. Efforts were made to develop conditions for the living polymerization of NBD by the use of proton trap and electron donor in the −35 to −60 °C range however this objective was only partially attained. The molecular weights increased linearly with conversion, and the rate was first‐order in confirmed monomer concentration up to approximately 25%; however, chain transfer became operational beyond this range. The microstructure of polynorbornadiene (PNBD) was investigated by high‐resolution 1 H and 13 C NMR spectroscopy. According to these techniques, the chain consisted of about equal amounts of exo/exo and exo/endo connected tricyclic repeat units. The head and tail groups were identified and quantitated, and this led to absolute molecular weight determination by integration. Molecular weights obtained by this method and by gel permeation chromatography (relative to polyisobutylene standards) were in good agreement. NMR spectroscopy indicated the presence of small but still identifiable amounts of branching units and their structures. The plot of the glass‐transition temperature against the reciprocal of the number‐average molecular weight was linear and yielded a glass‐transition temperature of 323 °C for the infinite molecular weight polymer. According to thermogravimetric analysis, PNBD was stable up to approximately 250 °C and showed a 5% weight loss at approximately 335 °C. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 732–739, 2003
Cost of breast cancer treatment. A 4-year longitudinal study. (1996)

The goal of mammography screening programs should be to achieve downstaging to stages 0 to 1 to achieve reduction in breast cancer mortality and to reduce the overall consumption of health care resources for the treatment of breast cancer. These cost data should be considered within the framework of future cost-effective analysis for screening mammography programs.
Loosely-coupled localization fusion system based on track-to-track fusion with bias alignment (2023)

The localization system is an essential element in robotics, which can provide accurate position information. Multiple localization systems can be integrated for reliable localization operations because there are various methods for measuring the position or processing algorithms. Significantly, the track-to-track (T2T) fusion method can fuse multiple localization systems using each system's estimate without accessing the sensor's low data. However, most T2T fusion-based localization systems ignore slowly varying biases, such as drift errors, odometry errors, and offsets among multiple maps. This can degrade the localization performance because a slowly varying bias is directly reflected in the localization estimate. Therefore, a slowly varying bias must be considered in the fusion process to derive reliable estimates. This study proposes a T2T fusion-based localization system that considers a slowly varying bias. First, the slow-varying bias difference between the systems was estimated. Because each localization system can have a different bias, the estimated bias difference was used to align it with the reference system. Second, a fused estimate can be obtained by T2T fusion using biasaligned estimates. The proposed fusion system can also be used without limiting the number of inputs to the localization system. The proposed system was compared with various T2T-based localization fusion algorithms for verification in a simulation environment, and it exhibited the best performance in RMSE error comparison.
Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders (2019)

Disruption of DMXL2 may predispose to NDDs including autism spectrum disorder. The robust interpretation of private variants requires a multifaceted approach that incorporates multigenerational pedigrees and genome-wide and population-scale data.
Magnetic Susceptibility and Mössbauer Emission Studies on the Relation between Structure and Degree of Hydration of Co(II)-5′IMP Complexes (1986)

Article Magnetic Susceptibility and Mössbauer Emission Studies on the Relation between Structure and Degree of Hydration of Co(II)-5′IMP Complexes was published on February 1, 1986 in the journal Zeitschrift für Physikalische Chemie (volume 149, issue 2).
Abstract 2846: Exploring ERBB3 as novel drug target in lung cancer (2012)

Abstract Recent evidences point to ERBB3 as a critical activator of the PI3K/Akt signaling axis and suggest that its trans-phosphorylation is linked to the occurrence of drug resistance in several cancers. Because of the absence of a functional tyrosine kinase, the best approach to target this receptor is through the development of selective monoclonal antibodies. For this purpose, our group has recently generated a set of mouse monoclonals with low nM affinity for human ERBB3. We have started to assess the effect of these antibodies in lung cancer using two systems: a) PC9 cells, known to be highly sensitive to gefitinib (IC50 0,03 uM), for the DelE746A750 in exon 19 of EGFR and its gefitinib-resistant counterpart PC9-ZD (Koizumi et al, 2005 Int J. Cancer 116, 36); b) primary lung adenocarcinoma cells isolated in our laboratory from Malignant Pleural Effusions (MPEs) and capable of efficient tumor propagation in vivo (Mancini et al, 2011, PlosONE 6: e21320). In PC9 cells anti-ERBB3 mabs, A3 and A4, strongly inhibit ligand-induced pHER3 and pAKT and induce receptor downmodulation. Furthermore, A3 and A4 potentiate the antiproliferative effect of gefitinib in a clonogenic assay, induce G0/G1 arrest, and increase the percentage of cells that undergo apoptosis. In the human primary MPE-derived lung adenocarcinoma culture PEd10, we observed that the expression of ERBB3 and its ligand are upregulated when cells are grown in spheroid vs adherent conditions. In this system, A3 and A4 antibodies significantly downmodulate spheroid propagation. Studies are ongoing to provide further insights as to the mechanism of action of anti-ERBB3 antibodies and to confirm efficacy in in vivo tumor models. Our results suggest that in a subset of lung adenocarcinomas which express high levels of ERBB3, this receptor contributes to cell growth and propagation and that targeting ERBB3 with antibodies capable of inducing receptor downmodulation can be considered a promising therapeutic approach. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2846. doi:1538-7445.AM2012-2846
Modulation of the immune response by antibacterial antibodies. (1983)

Antibodies induced by the gram+ bacteria Micrococcus lysodeikticus exhibit different carbohydrate specificities and hence might cross-react with membrane glycoproteins and/or glycolipids of mammalian cells. Using a T cell derived lymphoid line, these antibodies were found to detect a membrane marker which is only exposed in confluent culture conditions on non-dividing cells. Such confluence related antigen (Cag) is a cryptic membrane antigen, which can be unmasked through membrane perturbating agents such as p-formaldehyde or through interactions with macrophages and macrophage derived factors. Anti-micrococcus antibodies appear also to affect functionally normal T lymphocytes. Thus such reagents drastically inhibit the murine T cell reactivity towards mitogens such as Con A and PHA provided, however, the mitogenic signal is delivered through peritoneal macrophages. Furthermore, anti-micrococcus antibodies induce activated T lymphocytes into mitogenesis, but not unprimed resting T cells. Hence the physiological activity of anti-micrococcus antibodies depends on the state of activation of the T lymphocyte, indicating the involvement of cryptic membrane molecules. The relevance of such phenomena to host-bacteria and host-parasite interaction will be discussed.
Multi-resolution redundancy for error-resilient video transmission (2010)

In this paper we advocate a multi-resolution mechanism for redundant information generation and transmission with low overheads in bit-rate, in order to enable reliable video communication over challenging lossy networks with low latency. Our previous work entitled RECAP, transmitted a low resolution redundant version of a parent video stream, in order to achieve effective concealment of isolated and burst losses by clever multi-frame super-resolution processing at the decoder. A reference picture selection mechanism was used to transmit the low-resolution redundant video with high guarantee and stop drift in case of losses. In this work, we extend the framework to incorporate an additional distributed Wyner-Ziv coding layer on the low-resolution information to further correct errors, and consequently improve the error-concealed picture quality. The error-concealed super-resolved frame using the low-resolution information alone, now acts as side-information at the decoder to correct additional errors by decoding the Wyner-Ziv layer. Preliminary results are presented to demonstrate the efficacy of the proposed approach.
Programmable soft valves for digital and analog control (2022)

In soft devices, complex actuation sequences and precise force control typically require hard electronic valves and microcontrollers. Existing designs for entirely soft pneumatic control systems are capable of either digital or analog operation, but not both, and are limited by speed of actuation, range of pressure, time required for fabrication, or loss of power through pull-down resistors. Using the nonlinear mechanics intrinsic to structures composed of soft materials-in this case, by leveraging membrane inversion and tube kinking-two modular soft components are developed: a piston actuator and a bistable pneumatic switch. These two components combine to create valves capable of analog pressure regulation, simplified digital logic, controlled oscillation, nonvolatile memory storage, linear actuation, and interfacing with human users in both digital and analog formats. Three demonstrations showcase the capabilities of systems constructed from these valves: 1) a wearable glove capable of analog control of a soft artificial robotic hand based on input from a human user's fingers, 2) a human-controlled cushion matrix designed for use in medical care, and 3) an untethered robot which travels a distance dynamically programmed at the time of operation to retrieve an object. This work illustrates pathways for complementary digital and analog control of soft robots using a unified valve design.
The Discovery, Isolation, Elucidation of Structure, and Synthesis of Antamanide (1968)

Abstract Antamanide is the name we have given to a constituent of the fungus Amanita phalloides. This substance counteracts the lethal action of the Amanita toxins phalloidine and α‐amanatine if administered to the white mouse before, or simultaneously with, the poisons. Its concentration in the fungus is, however, so low that the toxic action of the latter predominates. Antamanide is a cyclic decapeptide formed from the L ‐amino acids alanine, phenylalanine, proline, and valine in the molar ratio 1:4:4:1. The amino‐acid sequence was determined by a combination of gas chromatography and mass spectrometry. The structural formula assigned was confirmed by synthesis according to a classic route of peptide chemistry.