gebhart/patrepeval huggingface dataset:
Learning to pour (2017)

Pouring is a simple task people perform daily. It is the second most frequently executed motion in cooking scenarios, after pick-and-place. We present a pouring trajectory generation approach, which uses force feedback from the cup to determine the future velocity of pouring. The approach uses recurrent neural networks as its building blocks. We collected the pouring demonstrations which we used for training. To test our approach in simulation, we also created and trained a force estimation system. The simulated experiments show that the system is able to generalize to single unseen element of the pouring characteristics.
Chemistry for the analysis of protein–protein interactions: Rapid and efficient cross-linking triggered by long wavelength light (1999)

Chemical cross-linking is a potentially useful technique for probing the architecture of multiprotein complexes. However, analyses using typical bifunctional cross-linkers often suffer from poor yields, and large-scale modification of nucleophilic side chains can result in artifactual results attributable to structural destabilization. We report here the de novo design and development of a type of protein cross-linking reaction that uses a photogenerated oxidant to mediate rapid and efficient cross-linking of associated proteins. The process involves brief photolysis of tris-bipyridylruthenium(II) dication with visible light in the presence of the electron acceptor ammonium persulfate and the proteins of interest. Very high yields of cross-linked products can be obtained with irradiation times of <1 second. This chemistry obviates many of the problems associated with standard cross-linking reagents.
Transfer of the bacterial gene for cytosine deaminase to mammalian cells confers lethal sensitivity to 5-fluorocytosine: a negative selection system. (1992)

Expression of the bacterial gene for cytosine deaminase (CD; EC 3.5.4.1) in mammalian cells was evaluated as a negative selection system or suicide vector for potential use in gene transfer studies and therapies. Mammalian cells, unlike certain bacteria and fungi, do not contain the enzyme CD and do not ordinarily metabolize cytosine to uracil. Nor do they metabolize the innocuous compound 5-fluorocytosine to the highly toxic compound 5-fluorouracil. The Escherichia coli CD gene underwent PCR oligonucleotide-directed mutagenesis to enhance its expression in a eukaryotic system and it was then cloned into an expression vector, pLXSN, that also contains a neomycin-resistance gene. Murine fibroblast lines were transfected with the plasmid and subjected to brief selection in the neomycin analogue G418. Lysates from these cell populations exhibited significant CD activity detected by conversion of radiolabeled cytosine to uracil. In clonogenic assays transfected cells expressing CD were selectively killed by incubation in 5-fluorocytosine, whereas control cell lines were not. Dose-response studies evaluating [3H]thymidine incorporation or cloning efficiency demonstrated profound inhibition at and above 65 micrograms of 5-fluorocytosine per ml. Mixed cellular assays showed that CD-positive cells could be eliminated without bystander killing of other cells. Retrovirus-mediated CD gene transfer into various tissues was also demonstrated. Thus CD, with its ability to produce the toxic antimetabolite 5-fluorouracil from 5-fluorocytosine, may be useful as a negative selection system for studies and treatments employing gene transfer techniques.
Chiral Lewis Acid-Catalyzed Enantioselective Intramolecular Carbonyl Ene Reactions of Unsaturated α-Keto Esters (2003)

[reaction: see text] Chiral Lewis acid-promoted highly enantioselective intramolecular carbonyl ene reactions of unsaturated alpha-keto esters have been investigated. In the presence of chiral Lewis acids such as [Sc((R,R)-Ph-pybox)](OTf)(3) and [Cu((S,S)-Ph-box)](OTf)(2), several unsaturated alpha-keto esters underwent carbonyl ene reactions in CH(2)Cl(2) at room temperature to give monocyclic products in good yield and excellent enantioselectivity.
Hodgkin and Reed-Sternberg cells in Hodgkin's disease represent the outgrowth of a dominant tumor clone derived from (crippled) germinal center B cells. (1996)

In Hodgkin's disease (HD), the Hodgkin and Reed-Sternberg (HRS) cells represent only a minute population in the diseased tissue. The investigation of lineage derivation and clonal origin of these cells has yielded conflicting results. We have analyzed HRS cells micromanipulated from infiltrated tissue sections of 10 primary HD patients for rearranged V genes, extending a previous study. Clonally related rearrangements were found in nine cases, indicating that HRS cells represent a dominant clone of B lineage-derived cells in at least a large fraction of cases of HD. Rearranged VH genes from HRS cells carried a high load of somatic mutation, indicating that HRS cells are derived from germinal center (GC) cells or their progeny. Stop codons in some in-frame V gene rearrangements suggest that the HRS cell precursors reside inside GCs, have acquired crippling mutations that prevent antigenic selection, but escape apoptosis through some transforming event.
Small Molecule Reversible Inhibitors of Bruton’s Tyrosine Kinase (BTK): Structure–Activity Relationships Leading to the Identification of 7-(2-Hydroxypropan-2-yl)-4-[2-methyl-3-(4-oxo-3,4-dihydroquinazolin-3-yl)phenyl]-9H-carbazole-1-carboxamide (BMS-935177) (2016)

Bruton's tyrosine kinase (BTK) belongs to the TEC family of nonreceptor tyrosine kinases and plays a critical role in multiple cell types responsible for numerous autoimmune diseases. This article will detail the structure-activity relationships (SARs) leading to a novel second generation series of potent and selective reversible carbazole inhibitors of BTK. With an excellent pharmacokinetic profile as well as demonstrated in vivo activity and an acceptable safety profile, 7-(2-hydroxypropan-2-yl)-4-[2-methyl-3-(4-oxo-3,4-dihydroquinazolin-3-yl)phenyl]-9H-carbazole-1-carboxamide 6 (BMS-935177) was selected to advance into clinical development.
Identification of residues required for ligand binding to the beta-adrenergic receptor. (1987)

The functional significance of conserved polar amino acids within the putative transmembrane region of the beta-adrenergic receptor (beta AR) was examined by oligonucleotide-directed mutagenesis of the hamster gene encoding beta AR and expression of the mutant genes in COS-7 cells. Although a substitution of aspartate at position 113 with an asparagine residue did not affect expression or processing of the protein, the resulting mutant beta AR did not show detectable binding toward the antagonist iodocyanopindolol. Replacement of the aspartate and asparagine residues at positions 79 and 318, respectively, had no effect on the affinity of the receptor toward antagonists but reduced the affinity of the receptor toward agonists by 1 order of magnitude. Furthermore, we observed that substitution of the proline at position 323 with a serine residue resulted in improper or incomplete processing of the beta AR, presumably reflecting a role for this residue in the folding of the receptor. Together with our previous results from deletion mutagenesis studies, these observations indicate that the ligand binding site involves the transmembrane region of the beta AR.
All-digital PAM impulse radio for multiple-access through frequency-selective multipath (2002)

Impulse radio (IR) is an ultra-wideband system with attractive features for baseband asynchronous multiple-access (MA), multimedia services, tactical wireless communications and networking. Implemented with analog components, the continuous-time IRMA model utilizes pulse-position modulation (PPM) and random time-hopping codes to alleviate multipath effects and suppress multiuser interference (MUI). We develop here a novel all-digital IRMA scheme and its discrete-time equivalent model that relies on pulse-amplitude modulation (PAM) and judiciously designed orthogonal user codes to eliminate MUI deterministically and account for frequency-selective multipath in the downlink. We also design a time-division-duplex access protocol and low-complexity linear multichannel receivers that we compare and test both analytically and by simulation.
<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology (2017)

Without a doubt, in the past 20 or so years, we have achieved the power of biology in different ways. In the present, we have many tools for developing novel technologies and applications for organism modifications that ultimately let us know many aspects of organisms’ biology and, therefore, apply that knowledge for technological purposes. Of all the model organisms and tools for genetic modification available, Escherichia coli stands out as a model organism and what we would like to call “molecular biologist tool box.” In the present chapter, we aim to review our current knowledge regarding genetic modifications and tools for modifying E. coli to generate plasmid vectors, single and multiple gene knockouts, whole genome editing, biosensor generation and applications and synthetic gene circuits and genomes.
Cell−Cell Junctions of Dermal Microvascular Endothelial Cells Contain Tight and Adherens Junction Proteins in Spatial Proximity (2004)

Endothelial cell-cell contacts control the vascular permeability, thereby regulating the flow of solutes, macromolecules, and leukocytes between blood vessels and interstitial space. Because of specific needs, the endothelial permeability differs significantly between the tight blood-brain barrier endothelium and the more permeable endothelial lining of the non-brain microvasculature. Most likely, such differences are due to a differing architecture of the respective interendothelial cell contacts. However, while the molecules and junctional complexes of macrovascular endothelial cells and the blood-brain barrier endothelium are fairly well characterized, much less is known about the organization of intercellular contacts of microvascular endothelium. Toward this end, we developed a combined cross-linking and immunoprecipitation protocol which enabled us to map nearest neighbor interactions of junctional proteins in the human dermal microvascular endothelial cell line HMEC-1. We show that proteins typically located in tight or adherens junctions of epithelial cells are in the proximity in HMEC-1 cells. This contrasts with the separation of the different types of junctions observed in polarized epithelial cells and "tight" endothelial layers of the blood-brain barrier and argues for a need of the specific junctional contacts in microvascular endothelium possibly required to support an efficient transendothelial migration of leukocytes.
Enzyme recruitment in vitro: use of cloned genes to extend the range of haloaromatics degraded by Pseudomonas sp. strain B13 (1984)

DNA fragments containing the xylD and xylL genes of TOL plasmid pWW0 -161 of Pseudomonas putida, which code for the catabolic enzymes toluate 1,2-dioxygenase and dihydrodihydroxybenzoic acid dehydrogenase, respectively, and the nahG gene of the NAH plasmid NAH7 , which codes for salicylate hydroxylase, were cloned in pBR322 vector plasmid. Deletion and insertion mutagenesis were used to localize these genes with respect to crucial endonuclease cleavage sites. The pBR322-based plasmids were ligated to the broad host range cloning vector pKT231 , or derivatives of it, and the hybrid plasmids were introduced into Pseudomonas sp. B13( WR1 ), a bacterium able to degrade 3-chlorobenzoate but not 4-chlorobenzoate, 3,5- dichlorobenzoate , salicylate, or chlorosalicylates . The cloned xylD gene expanded the catabolic range of WR1 to include 4-chlorobenzoate, whereas the cloned xylD - xylL genes enabled the isolation of derivatives of WR1 that degraded 3-chlorobenzoate, 4-chlorobenzoate, and 3,5- dichlorobenzoate . The cloned nahG gene extended the catabolic range of WR1 to include salicylate and 3-, 4-, and 5- chlorosalicylate .
Thiobarbiturates. II (1936)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThiobarbiturates. IIEllis Miller, James C. Munch, Frank S. Crossley, and Walter H. HartungCite this: J. Am. Chem. Soc. 1936, 58, 7, 1090–1091Publication Date (Print):July 1, 1936Publication History Published online1 May 2002Published inissue 1 July 1936https://pubs.acs.org/doi/10.1021/ja01298a007https://doi.org/10.1021/ja01298a007research-articleACS PublicationsRequest reuse permissionsArticle Views77Altmetric-Citations26LEARN 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
Mechanism of DnaB Helicase of Escherichia coli:  Structural Domains Involved in ATP Hydrolysis, DNA Binding, and Oligomerization (1999)

We describe the delineation of three distinct structural domains of the DnaB helicase of Escherichia coli: domain alpha, amino acid residues (aa) 1-156; domain beta, aa 157-302; and domain gamma, aa 303-471. Using mutants with deletion in these domains, we have examined their role(s) in hexamer formation, DNA-dependent ATPase, and DNA helicase activities. The mutant DnaBbetagamma protein, in which domain alpha was deleted, formed a hexamer; whereas the mutant DnaBalphabeta, in which domain gamma was deleted, could form only dimers. The dimerization of DnaBalphabeta was Mg(2+) dependent. These data suggest that the oligomerization of DnaB helicase involves at least two distinct protein-protein interaction sites; one of these sites is located primarily within domain beta (site 1), while the other interaction site is located within domain gamma (site 2). The mutant DnaBbeta, a polypeptide of 147 aa, where both domains alpha and gamma were deleted, displayed a completely functional ATPase activity. This domain, thus, constitutes the "central catalytic domain" for ATPase activity. The ATPase activity of DnaBalphabeta was kinetically comparable to that of DnaBbeta, indicating that domain alpha had little or no influence on the ATPase activity. In both cases, the ATPase activities were DNA independent. DnaBbetagamma had a DNA-dependent ATPase activity that was kinetically comparable to the ATPase activity of wild-type DnaB protein (wtDnaB), indicating a specific role for C-terminal domain gamma in enhancement of the ATPase activity of domain beta as well as in DNA binding. Mutant DnaBbetagamma, which lacked domain alpha, was devoid of any helicase activity pointing to a significant role for domain alpha. The major findings of this study are (i) domain beta contained a functional ATPase active site; (ii) domain gamma appeared to be the DNA binding domain and a positive regulator of the ATPase activity of domain beta; (iii) although domain alpha did not have any significant effect on the ATPase, DNA binding activities, or hexamer formation, it definitely plays a pivotal role in transducing the energy of ATP hydrolysis to DNA unwinding by the hexamer; and (iv) all three domains are required for helicase activity.
Distributed source coding using syndromes (DISCUS): design and construction (2003)

We address the problem of compressing correlated distributed sources, i.e., correlated sources which are not co-located or which cannot cooperate to directly exploit their correlation. We consider the related problem of compressing a source which is correlated with another source that is available only at the decoder. This problem has been studied in the information theory literature under the name of the Slepian-Wolf (1973) source coding problem for the lossless coding case, and as "rate-distortion with side information" for the lossy coding case. We provide a constructive practical framework based on algebraic trellis codes dubbed as DIstributed Source Coding Using Syndromes (DISCUS), that can be applicable in a variety of settings. Simulation results are presented for source coding of independent and identically distributed (i.i.d.) Gaussian sources with side information available at the decoder in the form of a noisy version of the source to be coded. Our results reveal the promise of this approach: using trellis-based quantization and coset construction, the performance of the proposed approach is 2-5 dB from the Wyner-Ziv (1976) bound.
The stimulants. (1992)

Stimulants are the most commonly prescribed psychotropic medications in child psychiatry, used generally for the treatment of attention deficit hyperactivity disorder (ADHD). In this article, the authors summarize the literature on the prevalence of use, neurobiology, and pharmacology of stimulants. Likewise, recent studies on the use of stimulants are reviewed, such as their use in specific ADHD populations including those with conduct disorder, girls, preschoolers, adolescents, and adults. Clinical guidelines for the management of children and adolescents receiving stimulants are offered, and treatment strategies are delineated for ADHD subjects with comorbidity and medication-induced adverse effects.
Characterization of an Extremely Large, Ligand-Induced Conformational Change in Plasminogen (1990)

Native human plasminogen has a radius of gyration of 39 angstroms. Upon occupation of a weak lysine binding site, the radius of gyration increases to 56 angstroms, an extremely large ligand-induced conformational change. There are no intermediate conformational states between the closed and open form. The conformational chang is not accompanied by a change in secondary structure, hence the closed conformation is formed by interaction between domains that is abolished upon conversion to the open form. This reversible change in conformation, in which the shape of the protein changes from that best described by a prolate ellipsoid to a flexible structure best described by a Debye random coil, is physiologically relevant because a weak lysine binding site regulates the activation of plasminogen.
Ripening-Related Gene from Avocado Fruit (1992)

Fruit ripening involves a series of changes in gene expression regulated by the phytohormone ethylene. AVOe3, a ripening-related gene in avocado fruit (Persea americana Mill. cv Hass), was characterized with regard to its ethylene-regulated expression. The AVOe3 mRNA and immunopositive protein were induced in mature fruit within 12 hours of propylene treatment. The AVOe3 mRNA levels reached a maximum 1 to 2 days before the ethylene climacteric, whereas the immunopositive protein continued to accumulate. RNA selected by the pAVOe3 cDNA clone encoded a polypeptide with molecular mass of 34 kilodaltons, corresponding to the molecular mass of the AVOe3 protein determined by immunoblots. The protein was soluble, remaining in solution at 100,000 gravity and eluted as a monomer on gel filtration. Because of its pattern of induction and relationship to an ethylene-related gene of tomato, the possible involvement of AVOe3 in ethylene biosynthesis is discussed.
Colocated antenna arrays: design desiderata for wireless communications (2003)

We report on in this paper is motivated by the drive towards antenna array miniaturization: going from an array of identical antennas that get spread out in space towards an array of colocalized antennas with differing responses. We address the problem of designing the colocated antenna array response for two applications: diversity reception using maximum ratio combining and MIMO communication capacity. The design criteria are derived under specific models regarding the distribution of the parameters of the frequency flat channel. We are particularly interested in evaluating the performance of two opposite extremes in terms of design: very selective beamspace type of operation versus spatially allpass antennas. We also show that the pathwise channel model converges for large number of paths to the stochastic channel model with separable correlation between TX and RX sides.
Engineering the Stem Cell Microenvironment (2007)

Multipotent stem cells in the body facilitate tissue regeneration, growth, and wound healing throughout life. The microenvironment in which they reside provides signals that direct these progenitors to proliferate, differentiate, or remain dormant; these factors include soluble molecules, the extracellular matrix, neighboring cells, and physical stimuli. Recent advances in the culture of embryonic stem cells and adult progenitors necessitate an increased understanding of these phenomena. Here, we summarize the interactions between stem cells and their local environment, drawing on in vivo observations and tissue culture studies. In addition, we describe novel methods of characterizing the effects of various environmental factors and review new techniques that enable scientists and engineers to more effectively direct stem cell fate.
Antibody Responses to Human Erythrocytes and Ovalbumin as Marker Traits of Disease Resistance in Dairy Calves (1989)

Microhemagglutination procedures were used to quantify antibody titers against human erythrocytes and ovalbumin in calf sera. Calves were also monitored for the prevalence of pneumonia and diarrhea. Calves, 72 males and 82 females, were the progeny of 15 AI bulls. Blood was sampled weekly for 2 wk after primary and secondary immunizations. Antibody response peaks to both antigens occurred by 14 and 7 d postimmunization, respectively. There were significant effects of season and birth and location of rearing on antibody titers against both test antigens. Diarrhea prevalence was negatively associated with high primary response antibody titers against human erythrocytes, but no trends were observed for pneumonia prevalence and for antibody titers to ovalbumin. Paternal half-sib heritability estimates ranged from 0 to .40 +/- .32 for primary antibody responses and from 0 to .87 +/- .50 for secondary antibody responses, depending on antibody specificity, and those for average titer were higher for antiovalbumin antibody (h2 = .48 +/- .39) than for antihuman erythrocyte antibody (h2 = .31 +/- .21). Although the environmental component of the humoral immune response is substantial, heritabilities of the magnitude in this study suggest the feasibility for successful genetic manipulation of antibody response profiles of young calves, and these may contribute to enhanced disease resistance.