gebhart/patrepeval huggingface dataset:
SE3-Pose-Nets: Structured Deep Dynamics Models for Visuomotor Planning and Control (2017)

In this work, we present an approach to deep visuomotor control using structured deep dynamics models. Our deep dynamics model, a variant of SE3-Nets, learns a low-dimensional pose embedding for visuomotor control via an encoder-decoder structure. Unlike prior work, our dynamics model is structured: given an input scene, our network explicitly learns to segment salient parts and predict their pose-embedding along with their motion modeled as a change in the pose space due to the applied actions. We train our model using a pair of point clouds separated by an action and show that given supervision only in the form of point-wise data associations between the frames our network is able to learn a meaningful segmentation of the scene along with consistent poses. We further show that our model can be used for closed-loop control directly in the learned low-dimensional pose space, where the actions are computed by minimizing error in the pose space using gradient-based methods, similar to traditional model-based control. We present results on controlling a Baxter robot from raw depth data in simulation and in the real world and compare against two baseline deep networks. Our method runs in real-time, achieves good prediction of scene dynamics and outperforms the baseline methods on multiple control runs. Video results can be found at: https://rse-lab.cs.washington.edu/se3-structured-deep-ctrl/
Modified embedded-atom potentials for cubic materials and impurities (1992)

In a comprehensive study, the modified embedded-atom method is extended to a variety of cubic materials and impurities. In this extension, all functions are analytic and computationally simple. The basic equations of the method are developed and applied to 26 elements: ten fcc, ten bcc, three diamond cubic, and three gaseous materials. The materials modeled include metals, semiconductors, and diatomic gases, all of which exhibit different types of bonding. Properties of these materials, including equation of state, elastic moduli, structural energies and lattice constants, simple defects, and surfaces, are calculated. The formalism for applying the method to combinations of these elements is developed and applied to the calculation of dilute heats of solution. In all cases, comparison is made to experiment or higher-level calculations when possible.
TCP/IP Illustrated Vol 1 The Protocols (2000)

TCP/IP Illustrated, Volume 1 is a complete and detailed guide to the entire TCP/IP protocol suite - with an important difference from other books on the subject. Rather than just describing what the RFCs say the protocol suite should do, this unique book uses a popular diagnostic tool so you may actually watch the protocols in action.By forcing various conditions to occur - such as connection establishment, timeout and retransmission, and fragmentation - and then displaying the results, TCP/IP Illustrated gives you a much greater understanding of these concepts than words alone could provide. Whether you are new to TCP/IP or you have read other books on the subject, you will come away with an increased understanding of how and why TCP/IP works the way it does, as well as enhanced skill at developing aplications that run over TCP/IP.
Mechanisms controlling the secretion and composition of exosomes (2016)

Los exosomas son pequenas vesiculas secretadas al medio extracelular por la mayor parte de celulas mediante la fusion de endosomas especificos llamados cuerpos multivesiculares (MVBs) con la membrana plasmatica. Actuan como mediadores de la comunicacion intercelular en multiples procesos biologicos tales como la respuesta inmune, la progresion tumoral y la cicatrizacion. Los exosomas contienen repertorios especificos de proteinas, mRNAs y miRNAs, que pueden ser transferidos y ser funcionales en las celulas receptoras. Sin embargo, se desconocian los mecanismos que controlan el empaquetamiento selectivo de moleculas, y mas concretamente de miRNAs, en exosomas. En este trabajo describimos pequenas secuencias de RNA (EXOmotifs) que estan presentes en determinados miRNAs y que controlan su empaquetamiento selectivo en exosomas. La proteina hnRNPA2B1 se une de forma especifica a miRNAs exosomales a traves de dichos EXOmotifs y controla su transporte a los exosomas. El empaquetamiento de miRNAs en exosomas se puede modular mediante la mutagenesis de los EXOmotifs indentificados o mediante cambios en los niveles de expresion de hnRNPA2B1. Ademas, describimos que hnRNPA2B1 se encuentra sumoilada en exosomas, y esta modificacion post-traduccional es importante para el empaquetamiento de miRNAs en exosomas. En este trabajo tambien identificamos al gen inducido por interferon 15 (ISG15) como un modificador post-traduccional implicado en el control de la secrecion de exosomas. Mediante el uso de ratones deficientes en ISG15 y ratones que expresan una forma enzimaticamente inactiva de la de-ISGilasa USP18, demostramos in vitro e in vivo que la conjugacion de ISG15 inhibe la secrecion de exosomas. La ISGilacion impide la secrecion de exosomas mediante la disminucion del numero de MVBs. La conjugacion de ISG15 no afecta a la biogenesis de MVBs pero induce su co-localizacion con lisosomas y promueve la agregacion y degradacion de proteinas. En consonancia, la inhibicion de la funcion lisosomal o la autofagia restaura la secrecion de exosomas pese a la induccion de ISG15. Especificamente, la ISGilacion de la proteina de MVBs TSG101 induce su agregacion y degradacion, y esto es suficiente para inhibir la secrecion de exosomas. Nuestro estudio muestra que hnRNPA2B1 es una proteina esencial en el transporte selectivo de miRNAs a los exosomas, y proporciona herramientas potenciales para el empaquetamiento de RNAs reguladores especificos en vesiculas extracelulares y su uso en aplicaciones biomedicas. Ademas en este trabajo identificamos la sumoilacion y la ISGilacion como nuevas modificaciones post-traduccionales implicadas en el control de la secrecion y la composicion de los exosomas.
In Vitro and In Vivo Gene Silencing by TransKingdom RNAi (tkRNAi) (2008)

RNA interference (RNAi) is a potent and specific mechanism for eliminating the mRNA of specific genes. This gene silencing mechanism occurs naturally and is highly conserved from plants to human cells, holding promise for functional genomics and for revolutionizing medicine due to its unlimited potential to treat genetic, epigenetic, and infectious disease. However, efforts to unleash the enormous potential of RNAi have met with significant challenges. Delivery is problematic because short interfering RNAs (siRNA) are negatively charged polymers that inefficiently enter cells and undergo rapid enzymatic degradation in vivo. In addition, the synthesis of siRNAs is expensive for long-term research and therapeutic applications. Recently, we have shown that nonpathogenic bacteria can be engineered to activate RNAi in mammalian cells (TransKingdom RNA interference; tkRNAi). This new approach offers several advantages and has significant implications. First, this method allows the establishment of a long-term stable gene silencing system in the laboratory against genes of interests in vitro and in vivo, and enables high-throughput functional genomics screening in mammalian systems. RNAi libraries can be constructed, stored, reproduced, amplified, and used with the help of E. coli as currently done with gene cloning. Second, this technology provides a clinically compatible way to achieve RNAi for therapeutic applications due to the proven clinical safety of nonpathogenic bacteria as a gene carrier. tkRNAi also eliminates the siRNA manufacture issue, and may circumvent or mitigate host interferon-like responses since siRNA is produced intracellularly.
Lineage tracing and characterization of insulin-secreting cells generated from adult pancreatic acinar cells (2005)

Although several studies have suggested that insulin-secreting cells can be generated in vitro from cells residing in adult exocrine pancreas, neither the origin of these cells nor their precise insulin secretory properties was obtained. We show here that insulin-secreting cells can be derived from adult mouse pancreatic exocrine cells by suspension culture in the presence of EGF and nicotinamide. The frequency of insulin-positive cells was only 0.01% in the initial preparation and increased to ≈5% in the culture conditions. Analysis by the Cre/loxP-based direct cell lineage tracing system indicates that these newly made cells originate from amylase/elastase-expressing pancreatic acinar cells. Insulin secretion is stimulated by glucose, sulfonylurea, and carbachol, and potentiation by glucagon-like peptide-1 also occurs. Insulin-containing secretory granules are present in these cells. In addition, we found that the enzymatic dissociation of pancreatic acini itself leads to activation of EGF signaling, and that inhibition of EGF receptor kinase blocks the transdifferentiation. These data demonstrate that pancreatic acinar cells can transdifferentiate into insulin-secreting cells with secretory properties similar to those of native pancreatic β cells, and that activation of EGF signaling is required in such transdifferentiation.
The high‐resolution X‐ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis (1987)

Triclinic crystals of the complex formed by eglin with subtilisin Carlsberg were analyzed by X-ray diffraction. The crystal and molecular structure of this complex was determined with data that extended to 0.12-nm resolution by a combination of Patterson search methods and isomorphous replacement techniques. Its structure was refined to a crystallographic R value of 0.178 (1.0-0.12 nm) using an energy-restraint least-squares procedure. The complete subtilisin molecule could be traced without ambiguity in the refined electron density. The eglin component, from which an amino-terminal segment is cleaved off, is only defined from Lys8I (i.e. the lysine residue 8 of the inhibitor) onwards. Per unit cell, 436 fixed solvent molecules and 2 calcium ions were located. In spite of 84 amino acid replacements and one deletion, subtilisin Carlsberg exhibits a very similar polypeptide fold to subtilisin BPN'. The root-mean-square deviations of all alpha-carbon atoms (excluding those at the deletion site) from models of subtilisin BPN' [Alden, R. A., Birktoft, J. J., Kraut, J., Robertus, J. D. & Wright, C. S. (1971) Biochem. Biophys. Res. Commun. 45, 337-344] and subtilisin Novo [Drenth, J., Hol, W. G. J., Jansonius, J. N. & Kockoek, R. (1972) Eur. J. Biochem. 25, 177-181] are 0.077 nm and 0.103 nm. Most of these deviations result from global shifts rather than changes of the local geometry. The single-residue deletion at position 56 affects only the surrounding conformation. Two sites of high electron density and close distances to surrounding oxygen ligands have been found in the Carlsberg enzyme which are probably occupied by calcium ions. Eglin consists of a twisted four-stranded beta-sheet flanked by an alpha-helix and by an exposed proteinase binding loop on opposite sides. Around the reactive site, Leu45I-Asp46I, this loop is mainly stabilized by electrostatic/hydrogen bond interactions with the side chains of two arginine residues which project from the hydrophobic core [Bode, W., Papamokos, E., Musil, D., Seemüller, W. & Fritz, H. (1986) EMBO J. 5, 813-818]. The reactive site loop conformation resembles that found in other 'small' proteinase inhibitors. The scissile peptide bond is not cleaved but its carbonyl group is slightly distorted from planar geometry. Most of the intermolecular contacts are contributed by the nine residues of the reactive-site loop Gly40I-Arg48I.(ABSTRACT TRUNCATED AT 400 WORDS)
A Requirement for Two Cell Types for Antibody Formation in vitro (1967)

A suspension of mouse spleen cells can be separated into two populations on the basis of their ability or inability to adhere to plastic dishes. It was found that both adherent and nonadherent cells were necessary for the induction of antibody formation to sheep red blood cells in vitro. Exposure of adherent cells to antigen for brief periods of time was sufficient to initiate a maximal in vitro response.
Circulating Fluidized Beds (2010)

In the last 20 years, significant improvements in the computational fluid dynamics (CFD) modeling have been made that allow the simulation of large-scale, commercial CFBs. Today, commercial codes are available that can model some of this behavior in large-scale, commercial units in a reasonable amount of time. However, the hydrodynamics in a riser or fluidized bed are complex with both micro and macroscale features. From particle clustering to large streamers to the core-annulus profile, the particle behavior in these unit operations rarely behaves as a “continuous fluid.” Even the role of particle size distribution is often neglected and models that do consider particle size distribution don’t always consider the role of particle size on granular temperature. Many models use insufficient boundary conditions by assuming uniform or symmetric profiles, which is rarely the case. Furthermore, grid sizing is usually based on computer limitations instead of model limitations, and many models of commercial systems extend beyond the capability of the constitutive equations being used. Successful application of today’s CFD models requires a good understanding of the equations behind the code, the assumptions used for those equations and the capability or limitations of the code. CFD is nothing more than a guess without an understanding of the fundamentals, underlying assumptions and code limitations that are part of every model.
A New in Vivo Cross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells (2014)

Protein-protein interactions (PPIs) are fundamental to the structure and function of protein complexes. Resolving the physical contacts between proteins as they occur in cells is critical to uncovering the molecular details underlying various cellular activities. To advance the study of PPIs in living cells, we have developed a new in vivo cross-linking mass spectrometry platform that couples a novel membrane-permeable, enrichable, and MS-cleavable cross-linker with multistage tandem mass spectrometry. This strategy permits the effective capture, enrichment, and identification of in vivo cross-linked products from mammalian cells and thus enables the determination of protein interaction interfaces. The utility of the developed method has been demonstrated by profiling PPIs in mammalian cells at the proteome scale and the targeted protein complex level. Our work represents a general approach for studying in vivo PPIs and provides a solid foundation for future studies toward the complete mapping of PPI networks in living systems.
Phase II Study of Imatinib Mesylate Plus Hydroxyurea in Adults With Recurrent Glioblastoma Multiforme (2005)

Imatinib mesylate plus hydroxyurea is well tolerated and associated with durable antitumor activity in some patients with recurrent GBM.
Tbx1: identification of a 22q11.2 gene as a risk factor for autism spectrum disorder in a mouse model (2011)

Although twin studies indicate clear genetic bases of autism spectrum disorder (ASD), the precise mechanisms through which genetic variations causally result in ASD are poorly understood. Individuals with 3 Mb and nested 1.5 Mb hemizygosity of the chromosome 22q11.2 represent genetically identifiable cases of ASD. However, because more than 30 genes are deleted even in the minimal deletion cases of 22q11.2 deficiency, the individual 22q11.2 gene(s) responsible for ASD remain elusive. Here, we examined the impact of constitutive heterozygosity of Tbx1, a 22q11.2 gene, on the behavioral phenotypes of ASD and characterized the regional and cellular expression of its mRNA and protein in mice. Congenic Tbx1 heterozygous (HT) mice were impaired in social interaction, ultrasonic vocalization, memory-based behavioral alternation, working memory and thigmotaxis, compared with wild-type (WT) mice. These phenotypes were not due to non-specific alterations in olfactory function, exploratory behavior, motor movement or anxiety-related behavior. Tbx1 mRNA and protein were ubiquitously expressed throughout the brains of C57BL/6J mice, but protein expression was enriched in regions that postnatally retain the capacity of neurogenesis, and in fact, postnatally proliferating cells expressed Tbx1. In postnatally derived hippocampal culture cells of C57BL/6J mice, Tbx1 levels were higher during proliferation than during differentiation, and expressed in neural progenitor cells, immature and matured neurons and glial cells. Taken together, our data suggest that Tbx1 is a gene responsible for the phenotypes of 22q11.2 hemizygosity-associated ASD possibly through its role in diverse cell types, including postnatally and prenatally generated neurons.
Vapor-Deposited Fluorinated Glycidyl Copolymer Thin Films with Low Surface Energy and Improved Mechanical Properties (2006)

Copolymer films of glycidyl methacrylate (GMA) with 2,2,3,3,4,4,5,5,6,6,7,7-dodecafluoroheptyl acrylate (DFHA) and with (perfluoroalkyl)ethyl methacrylate (PFEMA) were synthesized using initiated chemical vapor deposition (iCVD). By varying the inlet monomer feed ratios during iCVD process, the mole percentage of fluorinated acrylics in the P(GMA-co-DFHA) and P(GMA-co-PFEMA) copolymers was systematically varied between 19% and 65%. Vacuum annealing of the as-deposited copolymer films induced cross linking between epoxy functionalities of the GMA units. Both the hardness and the modulus of the annealed copolymers films were observed to increase with increasing GMA fraction, providing an order of magnitude improvement in these mechanical properties. The dispersive surface energy of the annealed copolymers showed a limited dependence on GMA fraction, with the range of values being 17.5−18.6 mN/m and 9.9−14.7 mN/m for the P(GMA-co-DHFA) and P(GMA-co-PFEMA) films, respectively. These data are as low as or lower than the benchmark value for poly(tetrafluoroethylene). The low surface energies and the limited dependence on composition suggest an enrichment of fluorinated units at the surface, a hypothesis which was directly verified using angle-resolved X-ray photoelectron spectroscopy. The annealed iCVD fluorinated copolymers also demonstrate optical transmission of greater than 99% in the visible spectrum for films with a thickness of 700 nm. The resulting combination of enhanced mechanical properties, low surface energy, and optical clarity is desirable for many applications.
Microbial indicators of aquatic ecosystem change: current applications to eutrophication studies (2003)

Human encroachment on aquatic ecosystems is increasing at an unprecedented rate. The impacts of human pollution and habitat alteration are most evident and of greatest concern at the microbial level, where a bulk of production and nutrient cycling takes place. Aquatic ecosystems are additionally affected by natural perturbations, including droughts, storms, and floods, the frequency and extent of which may be increasing. Distinguishing and integrating the impacts of natural and human stressors is essential for understanding environmentally driven change of microbial diversity and function. Microbial bioindicators play a major role in detecting and characterizing these changes. Complementary use of analytical and molecular indicator tools shows great promise in helping us clarify the processes underlying microbial population, community, and ecosystem change in response to environmental perturbations. This is illustrated in phytoplankton (microalgal and cyanobacterial) and bacterial community changes in a range of US estuarine and coastal ecosystems experiencing increasing development in their water- and airsheds as well as climatic changes (e.g., increasing hurricane frequency). Microbial indicators can be adapted to a range of monitoring programs, including ferries, moored instrumentation, and remote sensing, in order to evaluate environmental controls on microbial community structure and function over ecosystem to global scales.
Analysis of Collagen I, Iii, and Elastin in Abdominal Aortic Aneurysm of the Apoe -/- Mouse (2003)

Abdominal aortic aneurysms (AAAs) occur in up to 10% of the aged populations in industrialized nations. Early intervention in the disease process could have a significant impact on patient survival, but identifying newly forming aneurysms can be difficult. ApoE knockout mice develop AAAs following infusion of angiotensin II by osmotic minipump into the subcutaneous space of mice at doses ranging from 500 to 1000 ng/kg/ min for 7-28 days. These mice are used as models of AAA development. This study tested the hypothesis that near-IR spectrometry and PCR can determine AngII dose and collagen/elastin (C/E) ratio in mouse aortas.
Single Molecule Detection in Life Sciences (2000)

In recent years, the development of single molecule detection (SMD) techniques has opened up a new era of life science. The dynamic properties of biomolecules and the unique operations of molecular machines, which were hidden in averaged ensemble measurements, have been unveiled. The SMD techniques have rapidly been expanding to include a wide range of life science. The experiments on molecular motors, DNA transcription, enzyme reactions, protein dynamics, and cell signaling are summarized in this short review.
Missing data in spatiotemporal datasets: the UK rainfall chemistry network (2015)

Rainfall chemistry networks inevitably report some missing data, caused by contamination or loss of samples. However, there are no universally accepted rules about how such data, particularly from samples contaminated in the field, are identified and reported, leading to uncertainties in data usage by third parties, and possible incorrect inferences based on the reported data. This paper describes how the UK rainfall chemistry network data have been analysed for contamination, and how missing values can be estimated based on cross‐correlations in time and space, using data from 20 sites over 26 years. The final flagged dataset is available through the CEH Environmental Information Data Centre ( EIDC ). Erroneous data values are identified through consideration of ion balance (internal consistency), and evidence of contamination by birds or windblown dust based on the reported chemical analysis. Overall data capture with the erroneous data excluded and no replacement of missing data was 86%, but with much smaller data capture at some sites in some years, to &lt;30% in some cases. The use of estimated data to replace missing values resulted in an increase in overall data capture to 96%, with only one site having data capture &lt;70% in an individual year, and all sites achieving a data capture of 88% or more over the full period. The implications of using the reported ‘official’ annual data, as opposed to the dataset with missing values replaced by estimates, are illustrated by consideration of the temporal trend in nitrate at one site, which shows twice the value in the ‘official’ reported annual data compared with the ‘estimated’ data, part of a consistent pattern across all sites. Use of the uncorrected ‘raw’ sample data leads to large errors.