gebhart/patrepeval huggingface dataset:
X-Ray: Mechanical Search for an Occluded Object by Minimizing Support of Learned Occupancy Distributions (2020)

For applications in e-commerce, warehouses, healthcare, and home service, robots are often required to search through heaps of objects to grasp a specific target object. For mechanical search, we introduce X-Ray, an algorithm based on learned occupancy distributions. We train a neural network using a synthetic dataset of RGBD heap images labeled for a set of standard bounding box targets with varying aspect ratios. X-Ray minimizes support of the learned distribution as part of a mechanical search policy in both simulated and real environments. We benchmark these policies against two baseline policies on 1,000 heaps of 15 objects in simulation where the target object is partially or fully occluded. Results suggest that X-Ray is significantly more efficient, as it succeeds in extracting the target object 82% of the time, 15% more often than the best-performing baseline. Experiments on an ABB YuMi robot with 20 heaps of 25 household objects suggest that the learned policy transfers easily to a physical system, where it outperforms baseline policies by 15% in success rate with 17% fewer actions. Datasets, videos, and experiments are available at https://sites.google.com/berkeley.edu/x-ray.
Isolated venous thrombosis of inferior vena cava presenting Budd-Chiari syndrome associated with Behçet's disease: (2015)

A 29-year-old man was referred to our hospital with a 2-week history of general fatigue, upper abdominal pain, and bilateral leg oedema. For 3 years, he experienced recurrent oral aphtha ( Panel B ) and blurred vision. On admission, he presented erythema nodosum ( Panel C ), cutaneous venous distention over the …
Deterministic splitting of fluid volumes in electrowetting microfluidics (2012)

Conventional droplet generation approaches in digital microfluidics show ~10% variation in droplet volumes and are restricted to creating only small volumes. In this work, we demonstrate a new approach for splitting sample volumes precisely by gradually ramping down voltage, in place of abruptly switching off electrodes. This allows us to eliminate hydrodynamic instabilities responsible for variations in droplet volume. A simple visual method was developed for measuring sample volumes created on-chip. Our results show that generating and measuring arbitrary sample volumes accurately, with < 1% variation, is possible in electrowetting devices. The approach can be easily extended to existing digital microfluidic systems, and can potentially improve performance of applications requiring precise sample metering, such as immunoassays or DNA amplification.
Iron bioavailability from bouillon fortified with a novel ferric phytate compound: a stable iron isotope study in healthy women (part II) (2020)

Bouillon cubes are widely consumed and when fortified with iron could contribute in preventing iron deficiency. We report the development (part I) and evaluation (current part II) of a novel ferric phytate compound to be used as iron fortificant in condiments such as bouillon. Ferric pyrophosphate (FePP), is the compound of choice due to its high stability in foods, but has a modest absorption in humans. Our objective was to assess iron bioavailability from a novel iron fortificant consisting of ferric iron complexed with phytic acid and hydrolyzed corn protein (Fe-PA-HCP), used in bouillon with and without an inhibitory food matrix. In a randomised single blind, cross-over study, we measured iron absorption in healthy adult women (n = 22). In vitro iron bioaccessibility was assessed using a Caco-2 cell model. Iron absorption from Fe-PA-HCP was 1.5% and 4.1% in bouillon with and without inhibitory matrix, respectively. Relative iron bioavailability to FeSO<sub>4</sub> was 2.4 times higher than from FePP in bouillon (17% vs 7%) and 5.2 times higher when consumed with the inhibitory meal (41% vs 8%). Similar results were found in vitro. Fe-PA-HCP has a higher relative bioavailability versus FePP, especially when bouillon is served with an inhibitory food matrix.
iMet: Interactive Metric Learning in Healthcare Applications (2011)

Patient similarity assessment aims at providing a clinically meaningful distance measure for case retrieval in the context of clinical decision intelligence. Two of the key challenges are how to incorporate physician feedback with regard to the retrieval results and how to interactively update the underlying similarity measure based on the feedback. In this paper, we present the interactive Metric learning (iMet) method that can incrementally adjust the underlying distance metric based on latest supervision information. iMet is designed to scale linearly with the data set size based on matrix perturbation theory which allows the derivation of sound theoretical guarantees. We show empirical results demonstrating that iMet outperforms the baseline by three orders of magnitude in speed while obtaining comparable accuracy on several benchmark datasets. We also describe the application of the algorithm in a real world physician decision support system.
Evidence That the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution intga1 (2015)

teosinte glume architecture1 (tga1), a member of the SBP-box gene family of transcriptional regulators, has been identified as the gene conferring naked kernels in maize vs. encased kernels in its wild progenitor, teosinte. However, the identity of the causative polymorphism within tga1 that produces these different phenotypes has remained unknown. Using nucleotide diversity data, we show that there is a single fixed nucleotide difference between maize and teosinte in tga1, and this difference confers a Lys (teosinte allele) to Asn (maize allele) substitution. This substitution transforms TGA1 into a transcriptional repressor. While both alleles of TGA1 can bind a GTAC motif, maize-TGA1 forms more stable dimers than teosinte-TGA1. Since it is the only fixed difference between maize and teosinte, this alteration in protein function likely underlies the differences in maize and teosinte glume architecture. We previously reported a difference in TGA1 protein abundance between maize and teosinte based on relative signal intensity of a Western blot. Here, we show that this signal difference is not due to tga1 but to a second gene, neighbor of tga1 (not1). Not1 encodes a protein that has 92% amino acid similarity to TGA1 and that is recognized by the TGA1 antibody. Genetic mapping and phenotypic data show that tga1, without a contribution from not1, controls the difference in covered vs. naked kernels. No trait differences could be associated with the maize vs. teosinte alleles of not1. Our results document how morphological evolution can be driven by a simple nucleotide change that alters protein function.
THE EFFECT OF PHOTODYNAMIC THERAPY ON THE GLUTATHIONE LEVELS IN MACROPHAGES (1996)

Conference Abstract| November 01 1996 THE EFFECT OF PHOTODYNAMIC THERAPY ON THE GLUTATHIONE LEVELS IN MACROPHAGES Fiona M Ivison; Fiona M Ivison 1Centre for Photobiology and Photodynamic Therapy, Dept. Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT Search for other works by this author on: This Site PubMed Google Scholar David Vernon; David Vernon 1Centre for Photobiology and Photodynamic Therapy, Dept. Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT Search for other works by this author on: This Site PubMed Google Scholar Stan Brown Stan Brown 1Centre for Photobiology and Photodynamic Therapy, Dept. Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1996) 24 (4): 535S. https://doi.org/10.1042/bst024535sa Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Fiona M Ivison, David Vernon, Stan Brown; THE EFFECT OF PHOTODYNAMIC THERAPY ON THE GLUTATHIONE LEVELS IN MACROPHAGES. Biochem Soc Trans 1 November 1996; 24 (4): 535S. doi: https://doi.org/10.1042/bst024535sa Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1996 Biochemical Society1996 Article PDF first page preview Close Modal You do not currently have access to this content.
SPARC: Effect of Waveform on Kilohertz Frequency Nerve Block (2020)

There is growing interest in delivering kilohertz frequency (KHF) electrical signals to block conduction in autonomic nerves as a therapy to treat various diseases. Previous computational modeling, preclinical, and clinical studies used multiple different KHF waveforms to achieve block of the sciatic, vagus, and pudendal nerves. However, it remains unclear how the choice of waveform affects clinically relevant nerve block parameters. To address this knowledge gap, we quantified the effects of waveform on KHF block in vivo for the rat sciatic nerve, as well as in computational models of the rat sciatic nerve and the human vagus nerve. We compared block thresholds and onset responses across KHF sinusoids and charge‐balanced rectangular waveforms with different symmetries and duty cycles. Block thresholds were strongly dependent on the waveform shape. Experimentally, symmetric rectangular waveforms with full duty cycles had lower current thresholds for block than sinusoids, but they used slightly more power at threshold. Further, lower duty cycles yielded higher block thresholds, such that the log‐transformed block thresholds increased in an approximately linear manner as duty cycle decreased. The results from computational models were consistent with the in vivo block threshold relationships, although the models underestimated the increase in threshold with decreased duty cycle. While waveform selection had a clear and distinct effect on thresholds, it did not consistently affect in vivo onset response. Onset magnitude was similar across waveforms when normalized to block threshold. We also observed a history‐dependent reduction in onset response across all waveforms, from earlier trials with larger onset responses to later trials with reduced onsets during the course of a given experiment. Waveform had substantial effects on block thresholds but not on onset response. These quantitative data inform choice of waveform in subsequent studies and clinical applications. Such an understanding of the direct effects of KHF signal parameters on neural activity will enhance its effective use in therapeutic applications and facilitate the design of KHF stimulation parameters that achieve block with minimal undesired onset responses. Support or Funding Information NIH SPARC OT2 OD025340
Effects of poly(L-lactide-ε-caprolactone) and magnesium hydroxide additives on physico-mechanical properties and degradation of poly(L-lactic acid) (2016)

Therefore, the results demonstrated that the presence of PLCL and Mg(OH)2 additives in PLLA matrix could prevent the thermal decomposition and control degradation behavior of polyester.
Systematic Assessment of Patients With Unexplained Cardiac Arrest (2009)

Systematic clinical testing, including drug provocation and advanced imaging, results in unmasking of the cause of apparently unexplained cardiac arrest in >50% of patients. This approach assists in directing genetic testing to diagnose genetically mediated arrhythmia syndromes, which results in successful family screening.
Impact of systematic external birefringence on PMD (2005)

By simulation it is shown that fibers with a small intrinsic polarization mode dispersion (PMD) may be compromised more than those with large PMD when subject to a source of deterministic extrinsic birefringence, e.g. stress.
Molecular Containment and Mitigation of Genes within Crops — Prevention of Gene Establishment in Volunteer Offspring and Feral Strains (2005)

Jonathan Gressel and Hani Al-Ahmad Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel Email: Jonathan.Gressel@weizmann.ac.il 1. INTRODUCTION - NEEDS FOR PREVENTING GENE FLOW AND OVERCOMING FERALITY The previous chapters have indicated where the evolution of exo-ferality (ferality engendered by introgression of genes from relatives) and endo-ferality (back mutations within the crop) can be problems, both with traditionally bred and with transgenic crops. Below, we try to further delineate and accentuate ensuing problems, and then describe the status of potential molecular solutions. Molecular solutions to ferality problems for non-transgenic crops may sound oxymoronic in the present climate surrounding transgenics. Still, if the scientifically determined risk of the evolution of ferality in a crop outweighs the risk of having ferality-inhibiting transgenes in the crop, such molecular solutions should be sought. 1.1 MOLECULAR TOOLS TO PREVENT /OVERCOME FERALITY IN TRADITIONALLY BRED CROPS There are a variety of reasons to want to use molecular tools to prevent the evolution of feral forms of traditionally bred crops. Despite the popular press hysteria about “superweeds” evolving from transgenics, there have been many needs for preventing or overcoming ferality prior to the advent of transgenic crops. The feral sugar beet situation described in Chapter 4 is a case in point. Crops still not yet fully domesticated, where less domesticated forms can be volunteer
ChemInform Abstract: Opportunities in Nanotechnology via Organic Solid‐State Reactivity: Nanostructured Co‐Crystals and Molecular Capsules (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Retroesophageal Infracardiac Total Anomalous Pulmonary Venous Drainage (2017)

This case report describes the management of a term baby, born cyanotic, who was preoperatively diagnosed to have an obstructed total anomalous pulmonary venous drainage (TAPVD) in association with a functionally univentricular heart. An urgent repair of the anomalous pulmonary venous drainage was done, and a modified Blalock-Taussig shunt was constructed. Intraoperative difficulties were encountered when the pulmonary venous confluence was not seen in the usual location in the posterior mediastinal space, anterior to the esophagus. This report describes the rare finding of infracardiac TAPVD that is located in the retroesophageal space.
Hemoglobin Oxygen Saturation Tomography: Calibration in Phantom Studies and Patient Data Analysis (2002)

Oxygen saturation imaging has been calibrated relative to the measured pO2 values in tissue phantoms of Intralipid and blood. These calibration results are used to interpret the oxygen saturation of patient tumors and normal tissues.
Nanofabricated particles for engineered drug therapies: A preliminary biodistribution study of PRINT™ nanoparticles (2021)

A novel method for the fabrication of polymeric particles on the order of tens of nanometers to several microns is described. This imprint lithographic technique called PRINT™ (Particle Replication In Non-wetting Templates), takes advantage of the unique properties of elastomeric molds comprised of a low surface energy perfluoropolyether network, allowing the production of monodisperse, shape-specific nanoparticles from an extensive array of organic precursors. This engineered nature of particle production has a number of advantages over the construction of traditional nanoparticles such as liposomes, dendrimers, and colloidal precipitates. The gentle “top down” approach of PRINT enables the simultaneous and independent control over particle size and shape, composition, and surface functionality, and permits the loading of delicate cargos such as small organic therapeutics and biological macromolecules. Thus, this single tool serves as a comprehensive platform for the rational design and investigation of new nanocarriers in medicine, having applications ranging from therapeutics to advanced diagnostics. Preliminary in vitro and in vivo studies were conducted, demonstrating the future utility of PRINT particles as delivery vectors in nanomedicine. Monodisperse 200 nm poly(ethylene glycol)-based (PEG) particles were fabricated using PRINT methodology and characterized via scanning electron microscopy and dynamic light scattering. Incubation with HeLa cells showed very little cytotoxicity, even at high concentrations. The biodistribution and pharmacokinetics of [125I]-labeled particles were studied in healthy mice following bolus tail vein administration. The particles were distributed mainly to the liver and the spleen with an apparent distribution t1/2 of approximately 17 min followed by slow redistribution with a t1/2 of 3.3 h. The volume of distribution for the central and peripheral compartments was found to be approximately 3 mL and 5 mL, respectively.
Multi-Objective Optimization of Sensor Placement in Water Distribution Systems (2008)

Placement of water quality sensor has received an increasing concern/or timely providing the warning of possible contamination in a water system. Due to the large dimension of water distribution network and the difficulty for predicting where a contamination event occurs, it is a great challenge for engineers to come up with good sensor locations with any confidence to effectively detect possible contamination events. The problem is complicated by the fact that sensor location is evaluated against a number of objective criteria that may include the detection likelihood, the expected detection time, affected population and contaminated water consumption. A design that improves one objective may deteriorate another. In this paper, sensor placement is formulated as a multi objective optimization problem that is solved by using a competent genetic algorithm while the contamination events are simulated by the latest development of Monte Carlo method. This paper was presented at the 8th Annual Water Distribution Systems Analysis Symposium which was held with the generous support of Awwa Research Foundation (AwwaRF).
Abstract 1879: Pyrazolopyrimidines as novel selective allosteric MALT1 inhibitors with in vivo activity in ABC-DLBCL (2018)

Abstract Diffuse large B cell lymphoma (DLBCL) is the most common histological subtype of Non-Hodgkin's lymphoma, comprising 30% to 40% of all newly diagnosed cases. DLBCL is a biologically and clinically diverse disease with more than a dozen subtypes classified by the World Health Organization (WHO). Gene expression profiling groups DLBCL into three molecular subtypes, named according to their cell of origin, and which include germinal center B-cell-like (GCB) DLBCL, activated B-cell-like (ABC) DLBCL and primary mediastinal B cell lymphoma (PMBL). The current standard of care (SoC) is R-CHOP chemo-immunotherapy. Although the SoC is curative in a substantial proportion of patients, 40% of patients, especially in the ABC-DLBCL subtype, do not achieve durable remissions and suffer from progressive disease. In ABC-DLBCL, recurrent mutations in the B-cell receptor (BCR) and Toll-like receptor (TLR) pathways lead to constitutive NF-κB signaling. Mutations in the BCR pathway include gain-of-function mutations of CD79A/B (~20%) and CARD11 (~10%), and loss-of-function mutations of A20 (~25%). In the TLR pathway, MYD88 is commonly mutated (~37%). In recent years, knowledge of these aberrantly regulated pathways and their underlying mutations guided the development and investigation of newer molecular targeted agents, e.g. BTK, SYK, PI3K, PKC and MALT1 inhibitors. Among these strategies, inhibition of MALT1 provides the advantage that it is downstream of most of the reported BCR pathway mutations, including CARD11 mutations, and most of the targeted kinases with respect to potentially emerging resistance. However, no MALT1 inhibitor is in the clinic until now. Here, we report the identification of pyrazolopyrimidines as a new class of allosteric MALT1 inhibitors and their optimization for in vivo. The lead compound shows nanomolar potency in biochemical and cellular MALT1 protease reporter assays. In addition, pyrazolopyrimidines are highly selective for MALT1 and demonstrate differential cell killing of CARD11 mutant ABC-DLBCL cells vs control cells in proliferation assays. Furthermore, we demonstrate in vivo activity of pyrazolopyrimidines in CD79 and CARD11 mutant ABC-DLBCL xenograft models, with the lead compound causing regression in a CARD11 mutant xenograft model. Citation Format: Andreas Weiss, Thomas Radimerski, Daniel Wyss, Rita Andraos, Alexandra Buhles, Dario Sterker, Jean Quancard, Carole Pissot, Oliver Simic, Marc Bigaud, Frederic Bornancin, Achim Schlapbach, Catherine Regnier, Paul McSheehy, Elisabeth Buchdunger, Markus Wartmann, Martin Renatus, Ralf Endres, William Sellers, Francesco Hofmann. Pyrazolopyrimidines as novel selective allosteric MALT1 inhibitors with in vivo activity in ABC-DLBCL [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1879.
Thermal stability of Pb-alloy Josephson junction electrode materials. IX. Multilayered Pb–In–Au electrodes (1983)

Effects of substrate temperature, deposition sequence, and number of layers on the microstructure of Pb-12 wt. % In-4 wt. % Au films were studied using x-ray diffraction and transmission and scanning electron microscopy before and after repeated thermal cycling between 298 and 4.2 K. Significant grain size reduction and smooth film surfaces were obtained when the film deposition was carried out at substrate temperatures below 200 K. The deposition sequence strongly affected the rate of grain growth that occurred during warming from the deposition temperature to ambient temperature. It was found that the sequential Au and In depositions were essential in order to suppress grain growth. Strain introduced into films upon cooling from 298 to 4.2 K due to a thermal expansion coefficients mismatch between the films and Si substrates was also measured. The strain supported elastically by 0.35-μm-thick multilayered films was increased by reducing the thickness of each layer. By studying dependence of thickness of each layer on strain at 4.2 K, the critical grain size, smaller than which strain is not relaxed by dislocation glide, was determined to be ∼90 nm. This size agrees well with the previously measured mean spacing between misfit dislocations. Based on the present study, 10-layered Pb-In-Au films prepared at 200 K were developed for use as Josephson junction electrodes. The films had smooth surfaces and showed no undercut at the edges of lift-off patterned films. After 400 thermal cycles between 298 and 4.2 K, no microstructure changes such as hillock formation, dislocation slip steps, and grain rotation, were observed. These films can be used both as base electrode films for Pb-alloy Josephson junctions and as counterelectrodes for Nb/Pb-alloy junctions.