gebhart/patrepeval huggingface dataset:
Towards intuitive rigid-body physics through parameter search (2017)

The ability to predict the future location of objects is key for robots operating in unstructured and uncertain scenarios. It is even more important for general purpose humanoid robots that are meant to operate and adapt to multiple scenarios. They need to determine possible outcomes of actions, reason about their effect and plan subsequent movements accordingly to act preemptively. The prediction ability of current robotic systems in is far from that of humans. Neuroscience studies point out that humans have a predictive ability, called intuitive physics, to anticipate the behavior of dynamic environments enabling them to predict and take preemptive actions when necessary, for example to catch a flying ball or grab an object that is about to fall off a table. In this paper, we present a system that learns to predict based on previous observations. First, object's physical parameters are learned through observation using parameter search techniques. Second, the learned dynamic model of objects is used to generate probabilistic predictions through physics simulation. The parameter search update rules proposed, are compared to other approaches from the state-of-the-art in physical parameter learning. Finally, the predictive capability is evaluated through simulated and real experiments.
The dependence of poly-crystalline SiC mid-infrared optical properties on deposition conditions (2008)

We report on experimental measurements of the optical properties of thin films of poly-crystalline silicon carbide (poly-SiC) deposited by means of low pressure chemical vapor deposition (LPCVD). Measurements in the mid-IR region of the EM spectrum show strong dependence of both far field transmission and surface modes upon the deposition conditions including doping levels, ratio of dichlorosilane (DCS) to 1,3 disilabutane (DSB), and anneals performed on the film. We observe the link between the relative strength of near field phonon polariton resonances, the appearance of a polariton gap, and the achievement of extraordinary optical transmission (EOT).
IsmiR-29an oncogene or tumor suppressor in CLL? (2010)

B-cell chronic lymphocytic leukemia (CLL), the most common leukemia in the Western world. CLL occurs in two forms, aggressive and indolent. Aggressive CLL is characterized by high ZAP-70 expression and unmutated IgH V(H); indolent CLL shows low ZAP-70 expression and mutated IgH V(H). We recently found that miR-29 is up-regulated in indolent human B-CLL, compared to aggressive B-CLL and normal CD19(+) B-cells. To determine the role of miR-29 in CLL, we generated transgenic mice over-expressing miR-29 in mouse B-cells. Recently we reported that miR-29 transgenic mice develop indolent CLL phenotype. Interestingly, our previous findings suggest that miR-29 targets expression of TCL1, a critical oncogene in aggressive CLL, indicating that miR-29 might function as a tumor suppressor in CLL. Here we discuss these results and provide additional insights into function of miR-29 in CLL.
Cellular Kinetics of Perivascular MSC Precursors (2013)

Mesenchymal stem/stromal cells (MSCs) and MSC-like multipotent stem/progenitor cells have been widely investigated for regenerative medicine and deemed promising in clinical applications. In order to further improve MSC-based stem cell therapeutics, it is important to understand the cellular kinetics and functional roles of MSCs in the dynamic regenerative processes. However, due to the heterogeneous nature of typical MSC cultures, their native identity and anatomical localization in the body have remained unclear, making it difficult to decipher the existence of distinct cell subsets within the MSC entity. Recent studies have shown that several blood-vessel-derived precursor cell populations, purified by flow cytometry from multiple human organs, give rise to bona fide MSCs, suggesting that the vasculature serves as a systemic reservoir of MSC-like stem/progenitor cells. Using individually purified MSC-like precursor cell subsets, we and other researchers have been able to investigate the differential phenotypes and regenerative capacities of these contributing cellular constituents in the MSC pool. In this review, we will discuss the identification and characterization of perivascular MSC precursors, including pericytes and adventitial cells, and focus on their cellular kinetics: cell adhesion, migration, engraftment, homing, and intercellular cross-talk during tissue repair and regeneration.
ChemInform Abstract: ELECTRON‐TRANSFER PROCESSES. NEW SYNTHESIS OF Γ‐LACTONES BY PEROXYDISULFATE OXIDATION OF ISOPROPYLBENZENES AND ALIPHATIC CARBOXYLIC ACIDS (1981)

Abstract Die gleichzeitige Oxidation von Isopropylbenzol (I) und den aliphatischen Carbonsäuren (II) mit Peroxydisulfat in Gegenwart von F e(II)‐acetat und K‐Salzen der aliphatischen Säuren führen zu den γ‐Lactonen (III).
Development of media and recording technologies for 4×-speed DVD-R (2003)

We had been developing new medium and recording technology of DVD-R, DVD Recordable (write-once DVD) for 4/spl times/-speed recording. The essential technologies to realize the 4/spl times/-speed DVD-R we confirmed are described in this paper.
Synthesis and acetylcholinesterase inhibitory activity of several pyrimidone analogues of huperzine A (1995)

Syntheses of four new pyrimidone analogues of the acetylcholinesterase (AChE) inhibitor huperzine A are reported together with the inhibitory potencies of these compounds for foetal bovine calf serum AChE; β-lactone formation followed by a thermal cycloreversion reaction serves as the key step for introduction of the ethylidene appendage of 12 in the stereochemically correct form.
The Relevance of VDJ PCR Protocols in Detecting B-Cell Clonal Expansion in Lymphomas and Other Lymphoproliferative Disorders (1995)

VDJ PCR represents a useful and rapid technique to detect B-cell clonality in NHL, although with some differences depending on the NHL histotype and the panel of primers employed. The technique may also be of value to investigate the possible progression of early B-cell clonal expansion into frankly B-cell malignancy and to contribute to the controversy about the clonal lineage origin of the putative HD malignant cells.
Silicatein α: Cathepsin L-like protein in sponge biosilica (1998)

Earth's biota produces vast quantities of polymerized silica at ambient temperatures and pressures by mechanisms that are not understood. Silica spicules constitute 75% of the dry weight of the sponge Tethya aurantia, making this organism uniquely tractable for analyses of the proteins intimately associated with the biosilica. Each spicule contains a central protein filament, shown by x-ray diffraction to exhibit a highly regular, repeating structure. The protein filaments can be dissociated to yield three similar subunits, named silicatein alpha, beta, and gamma. The molecular weights and amino acid compositions of the three silicateins are similar, suggesting that they are members of a single protein family. The cDNA sequence of silicatein alpha, the most abundant of these subunits, reveals that this protein is highly similar to members of the cathepsin L and papain family of proteases. The cysteine at the active site in the proteases is replaced by serine in silicatein alpha, although the six cysteines that form disulfide bridges in the proteases are conserved. Silicatein alpha also contains unique tandem arrays of multiple hydroxyls. These structural features may help explain the mechanism of biosilicification and the recently discovered activity of the silicateins in promoting the condensation of silica and organically modified siloxane polymers (silicones) from the corresponding silicon alkoxides. They suggest the possibility of a dynamic role of the silicateins in silicification of the sponge spicule and offer the prospect of a new synthetic route to silica and siloxane polymers at low temperature and pressure and neutral pH.
System operations of mercury; a diode-pumped solid-state laser (2006)

The Mercury laser project is part of a national inertial fusion energy program in which four driver technologies are being considered including solid-state lasers, krypton fluoride gas lasers, Z-Pinch and heavy ions. Mercury's operational goals of 100 J, 10 Hz, 10% efficiency in a 5 times diffraction limited spot will demonstrate the critical technologies required for scaling the system to the multi-kilojoule level. Five one hour runs were conducted to assess system stability and reliability; energy fluctuations during the 55 J operations showed a 0.6% rms deviation. Current beam quality during average power operation is approximately 10 times diffraction limited. In the future, active wavefront control, and corrector plates for steady state thermal distortions will be implemented to achieve the 5 times diffraction limited spot.
Failure analysis of LSI using a scanning low-energy electron probe (1981)

The voltage contrast mode of SEM (scanning electron microscope) operation is a powerful diagnostic tool of LSI devices which have very small geometry of metal wirings and transistors. However, a conventional SEM uses a high energy electron probe (10 to 30 keV) which gives rise to radiation damage and charging effects to the LSI devices under investigation. We developed a new SEM which uses a low energy electron probe (0.5 to 7 keV) to overcome these problems. The instrument uses a field emission gun to minimize the deterioration of spatial resolution at low beam energy, and has the facility of mounting a probe card to energize an LSI device on a silicon wafer. Power sources and input signals to energize the LSI device under investigation are controlled by a dedicated computer. The SEM has a voltage resolution of about 0.5 V and a spatial resolution of about 0.05 μm with the probe current of 0.05 nA at 1 keV. We have analyzed many failures of LSI memory and logic circuits with several hundred gates by utilizing the SEM. The instrument can easily identify disconnects and bad voltage levels in LSI devices, while other methods (optical microscope observations, mechanical probings, and higher energy electron probes) cannot identify them. Moreover, the SEM is also useful for other devices such as printed circuit boards where wide metal wirings are covered with very thick insulator films (50 μm thick).
Bioactive Prenylhydroquinone Sulfates and a Novel C31 Furanoterpene Alcohol Sulfate from the Marine Sponge, Ircinia Sp. (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBioactive Prenylhydroquinone Sulfates and a Novel C31 Furanoterpene Alcohol Sulfate from the Marine Sponge, Ircinia Sp.Giuseppe Bifulco, Ines Bruno, Luigi Minale, Raffaele Riccio, Cécile Debitus, Genievieve Bourdy, Aude Vassas, and Jacques LavayreCite this: J. Nat. Prod. 1995, 58, 9, 1444–1449Publication Date (Print):September 1, 1995Publication History Published online1 July 2004Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/np50123a017https://doi.org/10.1021/np50123a017research-articleACS PublicationsRequest reuse permissionsArticle Views284Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Using Utility Functions to Control a Distributed Storage System (CMU-PDL-08-102) (2008)

Provisioning, and later optimizing, a storage system involves an extensive set of trade-offs between system metrics, including purchase cost, performance, reliability, availability, and power. Previous work has tried to simplify provisioning and tuning tasks by allowing a system administrator to specify goals for various storage metrics. While this helps by raising the level of specification from low-level mechanisms to high-level storage system metrics, it does not permit trade-offs between those metrics. This dissertation goes beyond goal-based requirements by allowing the system administrator to use a utility function to specify his objectives. Using utility, both the costs and benefits of configuration and tuning decisions can be examined within a single framework. This permits a provisioning system to make automated trade-offs across system metrics, such as performance, data protection and power consumption. It also allows an automated optimization system to properly balance the cost of data migration with its expected benefits. This work develops a prototype storage provisioning tool that uses an administrator-specified utility function to generate cost-effective storage configurations. The tool is then used to provide examples of how utility can be used to balance competing objectives (e.g., performance and data protection) and to provide guidance in the presence of external constraints. A framework for using utility to evaluate data migration is also developed. This framework balances data migration costs (decreases to current system metrics) against the potential benefits by discounting future expected utility. Experiments show that, by looking at utility over time, it is possible to choose the migration speed as well as weigh alternate optimization choices to provide the proper balance of current and future levels of service.
Long Chain Base-Acetyl Coenzyme A Acetyltransferase from the Microsomes of Hansenula ciferri (1972)

Microsomesof the yeast, Hansenula ciferri NRRL Y-1031, F-60-10, contain an enzyme (long chain base-acetyl coenzyme A acetyltransferase, EC 2.3 .1) which catalyzes the transfer of the acetyl moiety of acetyl coenzyme A to both the amino and hydroxyl groups of the sphingosine bases; a separation of these two transfer reactions could not be achieved.The enzyme also catalyzed an acetyl transfer to the hydroxyl groups of N-acetylated sphingosine bases and to the amino groups of normal aliphatic primary amines of 6 to 18 carbon atoms, but not to compounds such as p-nitroaniline, glucosamine, secondary amines, or primary alcohols.A similar enzyme was not found in rat organs nor in extracts of pigeon liver acetone powder.The reaction rates were directly proportional to enzyme concentration and time of incubation.The optimal pH depended on the type of buffer used.The reaction rates could be correlated to the charge conferred upon the micelles of the bases by the various buffers.The reaction was not reversible and an exchange between the products and substrates could not be shown.It was inhibited by coenzyme A but not by the lipid products.
Abstract P2083: Erk-mediated Phosphorylation Of Grk2 Leads To Reduced Pyruvate Dehydrogenase Activity And Alters Pyroptotic Signaling (2022)

G protein-coupled receptors (GPCRs) are important regulators of cellular functions where agonist binding leads to receptor conformational changes and downstream activation of g-protein-mediated signaling cascades. Signal transduction is terminated by receptor phosphorylation mediated by G-protein coupled receptor kinases (GRKs). GPCR kinase 2 (GRK2) is a main GRK in the heart and is upregulated in heart failure (HF) patients. Recently, we and others have shown that GRK2 can translocate to cardiac mitochondria where it regulates metabolism. Notably, we found that phosphorylated GRK2 at S670 post- ischemia/reperfusion (IR) decreases glucose mitochondrial utilization and pyruvate dehydrogenase (PDH) activity. Furthermore, 2D-SDS PAGE followed by LC/MS/MS revealed a potential link between mitochondrial GRK2 and PDH phosphorylation. Using a novel PDHα KI CRISPR Cas HEK cell line, we tested the hypothesize that PDH phosphorylation of this novel site was important for PDH activity. Utilizing cytosolic and mitochondrially-targeted pyruvate indicators we measured pyruvate levels in WT and KI HEK cells. In parallel, using a novel mouse model GRK2-S670A, we investigated the role of ERK in mediating GRK2 mitochondrial translocation and pyroptotic signaling. Further experiments will determine long-term impact of mitochondrial GRK2 in cell survival in cardiac pathological conditions.
From Social Machines to Social Protocols (2016)

The overarching vision of social machines is to facilitate social processes by having computers provide administrative support. We conceive of a social machine as a sociotechnical system (STS): a software-supported system in which autonomous principals such as humans and organizations interact to exchange information and services. Existing approaches for social machines emphasize the technical aspects and inadequately support the meanings of social processes, leaving them informally realized in human interactions. We posit that a fundamental rethinking is needed to incorporate accountability, essential for addressing the openness of the Web and the autonomy of its principals. We introduce Interaction-Oriented Software Engineering (IOSE) as a paradigm expressly suited to capturing the social basis of STSs. Motivated by promoting openness and autonomy, IOSE focuses not on implementation but on social protocols, specifying how social relationships, characterizing the accountability of the concerned parties, progress as they interact. Motivated by providing computational support, IOSE adopts the accountability representation to capture the meaning of a social machine's states and transitions.
Pyridine nucleotide metabolism in mammalian cells in culture (1973)

Abstract The biosynthesis of pyridine nucleotides has been examined in a number of mammalian cell lines in culture. In all lines examined, nicotinamide is incorporated by a biochemical pathway distinct from the Preiss‐Handler pathway for nicotinic acid. In at least the human cell line D98/AH2, there is no detectable endogenous synthesis of the pyridine ring from tryptophan. Although most cell lines examined (hamster BHK 21/13, mouse L929 and human D98/AH2) use either nicotinic acid or nicotinamide as a precursor for DPN and TPN, two mouse cell lines, 3T3‐4E and LM CIID, are unable to utilize nicotinic acid as a source of the pyridine ring. If nicotinic acid is present in the medium, substantial amounts of intracellular desamido DPN accumulate suggesting that the last step (desamido DPN→DPN) is limiting in the Preiss‐Handler pathway. With nicotinamide, the only compound which accumulates in substantial amounts apart from DPN and TPN is nicotinamide ribose; there is no detectable NMN. The results of pulse‐labeling experiments suggest that nicotinamide ribose may be an intermediate in the nicotinamide pathway. Following growth of D98/AH2 cells in high concentrations of niacin, biosynthesis of DPN from nicotinamide was completely inhibited for at least six hours. The converse experiment revealed no inhibition of niacin incorporation. This observation suggests that a niacin pathway intermediate, which present evidence indicates is desamido‐DPN. can inhibit nicotinamide utilization. Newly synthesized DPN turns over with a half‐life of two hours in azaserine‐treated D98/AH2 cells. In the absence of azaserine, the nicotinamide moiety of newly synthesized DPN is lost from D98/AH2 cells to the medium with a half‐life of eight hours. About 80% of the nicotinamide is lost to medium as nicotinamide ribose.
A Prototype Infant Incubator for Heliox Therapy (2006)

Heliox (Hx) gas has been shown to improve pulmonary function in infants, but methods for its delivery are invasive and problematic. To this end, we modified an Isolette (Hill-Rom Air-Shields) infant incubator (Hxl) to deliver Hx respiratory gas mixtures noninvasively while providing thermal stability for neonatal care in the Neonatal Intensive Care Unit (NICU). In vitro tests and in vivo animal studies were performed to compare the original design specifications and established baseline performance criteria for the Hxl design. The experimental environments at 50% and 80% relative humidity (RH) consisted of helium (He) with 21% and 50% O2 and control (C) of 21% and 50% O2 with the balance nitrogen (N). Elapsed times to steady state (SS) and recovery time back to SS (OCDss) due to opening and closing the door were recorded for each variable. All rabbits survived and appeared comfortable during all experimental conditions. These data show that the newly designed Isolette provides similar thermal, O2, CO2, and RH responses as the control incubator. Based on these positive safety/efficacy studies, study of the therapeutic impact of Hxl care on neonatal growth and development is in progress.
Advanced Lab-on-Fiber Optrodes Assisted by Oriented Antibody Immobilization Strategy (2022)

Lab-on-fiber (LoF) optrodes offer several advantages over conventional techniques for point-of-care platforms aimed at real-time and label-free detection of clinically relevant biomarkers. Moreover, the easy integration of LoF platforms in medical needles, catheters, and nano endoscopes offer unique potentials for in vivo biopsies and tumor microenvironment assessment. The main barrier to translating the vision close to reality is the need to further lower the final limit of detection of developed optrodes. For immune-biosensing purposes, the assay sensitivity significantly relies on the capability to correctly immobilize the capture antibody in terms of uniform coverage and correct orientation of the bioreceptor, especially when very low detection limits are requested as in the case of cancer diagnostics. Here, we investigated the possibility to improve the immobilization strategies through the use of hinge carbohydrates by involving homemade antibodies that demonstrated a significantly improved recognition of the antigen with ultra-low detection limits. In order to create an effective pipeline for the improvement of biofunctionalization protocols to be used in connection with LoF platforms, we first optimized the protocol using a microfluidic surface plasmon resonance (mSPR) device and then transferred the optimized strategy onto LoF platforms selected for the final validation. Here, we selected two different LoF platforms: a biolayer interferometry (BLI)-based device (commercially available) and a homemade advanced LoF biosensor based on optical fiber meta-tips (OFMTs). As a clinically relevant scenario, here we focused our attention on a promising serological biomarker, Cripto-1, for its ability to promote tumorigenesis in breast and liver cancer. Currently, Cripto-1 detection relies on laborious and time-consuming immunoassays. The reported results demonstrated that the proposed approach based on oriented antibody immobilization was able to significantly improve Cripto-1 detection with a 10-fold enhancement versus the random approach. More interestingly, by using the oriented antibody immobilization strategy, the OFMTs-based platform was able to reveal Cripto-1 at a concentration of 0.05 nM, exhibiting detection capabilities much higher (by a factor of 250) than those provided by the commercial LoF platform based on BLI and similar to the ones shown by the commercial and well-established bench-top mSPR Biacore 8K system. Therefore, our work opened new avenues into the development of high-sensitivity LoF biosensors for the detection of clinically relevant biomarkers in the sub-ng/mL range.
Early‐onset atopy is associated with enhanced lymphocyte cytokine responses in 11‐year‐old children (2007)

Early age at sensitization is associated with enhanced T cell cytokine responses and indices of adverse asthma outcome. T cell cytokine responses might be programmed at the time of initial atopic sensitization.